Class: Rafflesia::Sequences

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

Instance Method Summary collapse

Constructor Details

#initialize(client) ⇒ Sequences

Returns a new instance of Sequences.



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

def initialize(client)
  @client = client
end

Instance Method Details

#alignmentsAlign(query:, target:, gap: nil, match: nil, mismatch: nil, query_positions: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSequenceAlignData

POST /v1/sequences/alignments/align

Parameters:

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

    Gap penalty (default -2)

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

    Match score (default 1)

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

    Mismatch penalty (default -1)

  • query (String) —

    Sequence ID or local FASTA path for query sequence

  • query_positions (Array<Integer>, nil) (defaults to: nil) —

    Optional 1-based query residue positions to project through the alignment; input order and duplicates are preserved.

  • target (String) —

    Sequence ID or local FASTA path for target sequence

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 22

def alignmentsAlign(
  query:,
  target:,
  gap: nil,
  match: nil,
  mismatch: nil,
  query_positions: nil,
  request_options: {}
)
  body = {
    'gap' => gap,
    'match' => match,
    'mismatch' => mismatch,
    'query' => query,
    'query_positions' => query_positions,
    'target' => target
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/alignments/align',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSequenceAlignData.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

#catalogsBuild(name:, version:, dataset_name: nil, dataset_version: nil, input_object_id: nil, input_path: nil, source_database_snapshot: nil, source_tool_version: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSequenceCatalogBuildData

POST /v1/sequences/catalogs/build

Parameters:

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

    Optional dataset name carried into catalog provenance

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

    Optional dataset version carried into catalog provenance

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

    Object id containing input FASTA bytes

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

    Input FASTA path

  • name (String) —

    Logical catalog name, for example uniprot_swissprot

  • source_database_snapshot (Rafflesia::DatabaseSnapshot, nil) (defaults to: nil) —

    Optional source database snapshot that produced the FASTA

  • source_tool_version (Rafflesia::ToolVersion, nil) (defaults to: nil) —

    Optional source tool version that produced the FASTA

  • version (String) —

    Immutable catalog version or source snapshot

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 62

def catalogsBuild(
  name:,
  version:,
  dataset_name: nil,
  dataset_version: nil,
  input_object_id: nil,
  input_path: nil,
  source_database_snapshot: nil,
  source_tool_version: nil,
  request_options: {}
)
  body = {
    'dataset_name' => dataset_name,
    'dataset_version' => dataset_version,
    'input_object_id' => input_object_id,
    'input_path' => input_path,
    'name' => name,
    'source_database_snapshot' => source_database_snapshot,
    'source_tool_version' => source_tool_version,
    'version' => version
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/catalogs/build',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSequenceCatalogBuildData.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

#catalogsInspect(catalog_id: nil, catalog_object_id: nil, name: nil, version: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSequenceCatalogInspectData

POST /v1/sequences/catalogs/inspect

Parameters:

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

    Deterministic sequence catalog id

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

    Sequence catalog manifest object id

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

    Catalog name to resolve through the local catalog registry

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

    Catalog version to resolve through the local catalog registry

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 102

def catalogsInspect(
  catalog_id: nil,
  catalog_object_id: nil,
  name: nil,
  version: nil,
  request_options: {}
)
  body = {
    'catalog_id' => catalog_id,
    'catalog_object_id' => catalog_object_id,
    'name' => name,
    'version' => version
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/catalogs/inspect',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSequenceCatalogInspectData.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

#catalogsList(name: nil, version: nil, limit: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSequenceCatalogListData

GET /v1/sequences/catalogs/list

Parameters:

  • name (String, nil) (defaults to: nil)
  • version (String, nil) (defaults to: nil)
  • limit (Integer, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 133

def catalogsList(
  name: nil,
  version: nil,
  limit: nil,
  request_options: {}
)
  params = {
    'name' => name,
    'version' => version,
    'limit' => limit
  }.compact
  response = @client.request(
    method: :get,
    path: '/v1/sequences/catalogs/list',
    auth: true,
    params: params,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSequenceCatalogListData.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

#indexesBlastBuild(name:, version:, allow_unbenchmarked_publish: nil, blastdb_version: nil, dry_run: nil, extra_args: nil, index_format: nil, input_file_name: nil, input_object_id: nil, input_path: nil, molecule: nil, output_dir: nil, parse_seqids: nil, register_manifest: nil, store_artifacts: nil, title: nil, request_options: {}) ⇒ Rafflesia::EnvelopeBlastDbBuildData

POST /v1/sequences/indexes/blast/build

Parameters:

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

    Unsafe local/dev escape hatch: allow register_manifest to publish a rafflesia_pack manifest without benchmark evidence.

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

    BLAST DB version; defaults to 5

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

    Return the deterministic plan without executing makeblastdb

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

    Explicit additional makeblastdb arguments

  • index_format (Rafflesia::Types::BlastDbBuildRequestIndexFormat, nil) (defaults to: nil) —

    Index format to build; blastdb uses makeblastdb, rafflesia_pack builds a protein pack consumed by rafflesia_blastp

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

    Optional filename to use when materializing input_object_id

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

    Object id for an input FASTA artifact

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

    Input FASTA path

  • molecule (Rafflesia::Types::BlastDbBuildRequestMolecule, nil) (defaults to: nil) —

    BLAST molecule type; defaults to prot

  • name (String) —

    Logical database name, for example uniprot_swissprot

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

    Directory for generated BLAST DB files and manifest

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

    Pass -parse_seqids to makeblastdb

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

    Whether to publish the manifest into the local BLAST DB registry after build

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

    Whether to store generated artifacts in the object store; defaults to true

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

    Optional makeblastdb title

  • version (String) —

    Immutable logical database version

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 175

def indexesBlastBuild(
  name:,
  version:,
  allow_unbenchmarked_publish: nil,
  blastdb_version: nil,
  dry_run: nil,
  extra_args: nil,
  index_format: nil,
  input_file_name: nil,
  input_object_id: nil,
  input_path: nil,
  molecule: nil,
  output_dir: nil,
  parse_seqids: nil,
  register_manifest: nil,
  store_artifacts: nil,
  title: nil,
  request_options: {}
)
  body = {
    'allow_unbenchmarked_publish' => allow_unbenchmarked_publish,
    'blastdb_version' => blastdb_version,
    'dry_run' => dry_run,
    'extra_args' => extra_args,
    'index_format' => index_format,
    'input_file_name' => input_file_name,
    'input_object_id' => input_object_id,
    'input_path' => input_path,
    'molecule' => molecule,
    'name' => name,
    'output_dir' => output_dir,
    'parse_seqids' => parse_seqids,
    'register_manifest' => register_manifest,
    'store_artifacts' => store_artifacts,
    'title' => title,
    'version' => version
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/blast/build',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeBlastDbBuildData.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

#indexesBlastDescribe(manifest_path: nil, ref: nil, request_options: {}) ⇒ Rafflesia::EnvelopeBlastDbDescribeData

POST /v1/sequences/indexes/blast/describe

Parameters:

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

    Local manifest path

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

    Published DB ref such as name:version or manifest object id

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 229

def indexesBlastDescribe(
  manifest_path: nil,
  ref: nil,
  request_options: {}
)
  body = {
    'manifest_path' => manifest_path,
    'ref' => ref
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/blast/describe',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeBlastDbDescribeData.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

#indexesBlastEvict(dry_run: nil, manifest_path: nil, max_bytes: nil, policy: nil, ref: nil, target_dir: nil, request_options: {}) ⇒ Rafflesia::EnvelopeBlastDbEvictData

POST /v1/sequences/indexes/blast/evict

Parameters:

  • dry_run (Boolean, nil) (defaults to: nil)
  • manifest_path (String, nil) (defaults to: nil)
  • max_bytes (Integer, nil) (defaults to: nil) —

    If positive, evict oldest selected cache files until selected cache bytes are less than or equal to this limit. Zero evicts every selected file.

  • policy (Rafflesia::CacheEvictionPolicy, nil) (defaults to: nil) —

    Optional cache policy for TTL and pinned-path eviction controls.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 259

def indexesBlastEvict(
  dry_run: nil,
  manifest_path: nil,
  max_bytes: nil,
  policy: nil,
  ref: nil,
  target_dir: nil,
  request_options: {}
)
  body = {
    'dry_run' => dry_run,
    'manifest_path' => manifest_path,
    'max_bytes' => max_bytes,
    'policy' => policy,
    'ref' => ref,
    'target_dir' => target_dir
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/blast/evict',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeBlastDbEvictData.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

#indexesBlastList(limit: nil, request_options: {}) ⇒ Rafflesia::EnvelopeBlastDbListData

GET /v1/sequences/indexes/blast/list

Parameters:

  • limit (Integer, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 292

def indexesBlastList(
  limit: nil,
  request_options: {}
)
  params = {
    'limit' => limit
  }.compact
  response = @client.request(
    method: :get,
    path: '/v1/sequences/indexes/blast/list',
    auth: true,
    params: params,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeBlastDbListData.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

#indexesBlastMaterialize(manifest_path: nil, ref: nil, target_dir: nil, verify: nil, request_options: {}) ⇒ Rafflesia::EnvelopeBlastDbMaterializeData

POST /v1/sequences/indexes/blast/materialize

Parameters:

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

    Local manifest path

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

    Published DB ref such as name:version or manifest object id

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

    Directory used as the local BLAST DB cache

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

    Verify materialized files by SHA-256

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 318

def indexesBlastMaterialize(
  manifest_path: nil,
  ref: nil,
  target_dir: nil,
  verify: nil,
  request_options: {}
)
  body = {
    'manifest_path' => manifest_path,
    'ref' => ref,
    'target_dir' => target_dir,
    'verify' => verify
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/blast/materialize',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeBlastDbMaterializeData.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

#indexesBlastPublish(allow_unbenchmarked_publish: nil, benchmark_object_id: nil, manifest_object_id: nil, manifest_path: nil, max_local_control_bytes: nil, max_object_bytes: nil, max_object_reads: nil, min_byte_reduction_fraction: nil, min_hit_overlap_fraction: nil, min_recall_at_1: nil, min_recall_at_10: nil, ref: nil, require_benchmark: nil, require_exact_pack_reads: nil, require_no_local_control_files: nil, require_zero_materialization: nil, request_options: {}) ⇒ Rafflesia::EnvelopeBlastDbPublishData

POST /v1/sequences/indexes/blast/publish

Parameters:

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

    Unsafe local/dev escape hatch: allow publishing a rafflesia_pack manifest without benchmark evidence.

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

    Object id of a BLAST search benchmark artifact produced by sequences.search.blast.benchmark

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

    Manifest object id

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

    Local manifest path

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

    Optional publish gate threshold for object-native local control bytes

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

    Optional publish gate threshold for object-native object bytes fetched

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

    Optional publish gate threshold for object-native object reads

  • min_byte_reduction_fraction (Float, nil) (defaults to: nil) —

    Optional publish gate threshold for object-native byte reduction versus the materialized baseline

  • min_hit_overlap_fraction (Float, nil) (defaults to: nil) —

    Optional publish gate threshold for full hit-overlap fraction against the materialized BLAST baseline

  • min_recall_at_1 (Float, nil) (defaults to: nil) —

    Optional publish gate threshold for object-native recall@1 against the materialized BLAST baseline

  • min_recall_at_10 (Float, nil) (defaults to: nil) —

    Optional publish gate threshold for object-native recall@10 against the materialized BLAST baseline

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

    Published DB ref override

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

    Require a passing BLAST object-native benchmark artifact before publishing

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

    Require benchmark evidence that exact scoring read Rafflesia pack sequence objects directly

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

    Require benchmark evidence that object-native exact scoring wrote no local candidate/control files

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

    Require benchmark evidence that object-native search materialized zero local database bytes

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 362

def indexesBlastPublish(
  allow_unbenchmarked_publish: nil,
  benchmark_object_id: nil,
  manifest_object_id: nil,
  manifest_path: nil,
  max_local_control_bytes: nil,
  max_object_bytes: nil,
  max_object_reads: nil,
  min_byte_reduction_fraction: nil,
  min_hit_overlap_fraction: nil,
  min_recall_at_1: nil,
  min_recall_at_10: nil,
  ref: nil,
  require_benchmark: nil,
  require_exact_pack_reads: nil,
  require_no_local_control_files: nil,
  require_zero_materialization: nil,
  request_options: {}
)
  body = {
    'allow_unbenchmarked_publish' => allow_unbenchmarked_publish,
    'benchmark_object_id' => benchmark_object_id,
    'manifest_object_id' => manifest_object_id,
    'manifest_path' => manifest_path,
    'max_local_control_bytes' => max_local_control_bytes,
    'max_object_bytes' => max_object_bytes,
    'max_object_reads' => max_object_reads,
    'min_byte_reduction_fraction' => min_byte_reduction_fraction,
    'min_hit_overlap_fraction' => min_hit_overlap_fraction,
    'min_recall_at_1' => min_recall_at_1,
    'min_recall_at_10' => min_recall_at_10,
    'ref' => ref,
    'require_benchmark' => require_benchmark,
    'require_exact_pack_reads' => require_exact_pack_reads,
    'require_no_local_control_files' => require_no_local_control_files,
    'require_zero_materialization' => require_zero_materialization
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/blast/publish',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeBlastDbPublishData.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

#indexesBlastVerify(manifest_path: nil, ref: nil, target_dir: nil, request_options: {}) ⇒ Rafflesia::EnvelopeBlastDbVerifyData

POST /v1/sequences/indexes/blast/verify

Parameters:

  • manifest_path (String, nil) (defaults to: nil)
  • ref (String, nil) (defaults to: nil)
  • target_dir (String, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 417

def indexesBlastVerify(
  manifest_path: nil,
  ref: nil,
  target_dir: nil,
  request_options: {}
)
  body = {
    'manifest_path' => manifest_path,
    'ref' => ref,
    'target_dir' => target_dir
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/blast/verify',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeBlastDbVerifyData.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

#indexesCandidatesApply(namespace:, build_policy: nil, dataset_name: nil, dataset_version: nil, decision_object_id: nil, decision_path: nil, input_object_id: nil, input_path: nil, name: nil, timeout_ms: nil, version: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSequenceCandidateApplyData

POST /v1/sequences/indexes/candidates/apply

Parameters:

  • build_policy (Rafflesia::Types::SequenceCandidateApplyRequestBuildPolicy, nil) (defaults to: nil) —

    Immutable publish policy for the canonical namespace. Defaults to if_not_exists.

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

    Optional dataset name override carried into build provenance.

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

    Optional dataset version override carried into build provenance.

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

    Object id containing a sequence candidate decision artifact.

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

    Local JSON path containing a sequence candidate decision artifact.

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

    Optional FASTA source object override.

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

    Optional FASTA source override readable by the API server.

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

    Optional logical name override carried into build provenance.

  • namespace (String) —

    Canonical namespace to build with the selected layout.

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

    Hard deadline for applying the selected layout in milliseconds.

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

    Optional logical version override carried into build provenance.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 454

def indexesCandidatesApply(
  namespace:,
  build_policy: nil,
  dataset_name: nil,
  dataset_version: nil,
  decision_object_id: nil,
  decision_path: nil,
  input_object_id: nil,
  input_path: nil,
  name: nil,
  timeout_ms: nil,
  version: nil,
  request_options: {}
)
  body = {
    'build_policy' => build_policy,
    'dataset_name' => dataset_name,
    'dataset_version' => dataset_version,
    'decision_object_id' => decision_object_id,
    'decision_path' => decision_path,
    'input_object_id' => input_object_id,
    'input_path' => input_path,
    'name' => name,
    'namespace' => namespace,
    'timeout_ms' => timeout_ms,
    'version' => version
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/candidates/apply',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSequenceCandidateApplyData.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

#indexesCandidatesBenchmark(namespace:, max_hits: nil, max_object_bytes_per_query: nil, max_object_reads_per_query: nil, min_recall_at_k: nil, min_top_hit_identity: nil, queries_object_id: nil, queries_path: nil, query_mode: nil, require_top_hit_id_matches_query_id: nil, require_zero_materialization: nil, store_artifact: nil, timeout_ms: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSequenceCandidateBenchmarkData

POST /v1/sequences/indexes/candidates/benchmark

Parameters:

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

    Maximum hits per query; defaults to 10.

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

    Optional pass threshold for object bytes fetched per query.

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

    Optional pass threshold for object reads per query.

  • min_recall_at_k (Float, nil) (defaults to: nil) —

    Optional minimum mean recall@k against exact_safe search.

  • min_top_hit_identity (Float, nil) (defaults to: nil) —

    Optional minimum identity for each query top hit.

  • namespace (String) —

    Sequence candidate namespace to benchmark.

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

    Object id containing benchmark query FASTA bytes.

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

    Multi-record FASTA path containing benchmark queries.

  • query_mode (Rafflesia::Types::SequenceCandidateBenchmarkRequestQueryMode, nil) (defaults to: nil) —

    Seed serving mode used for each query.

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

    Require each query record id to match the top returned sequence id.

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

    Require every query to report zero materialized database bytes.

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

    Whether to store the benchmark JSON artifact in the object store; defaults to true.

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

    Hard deadline for this benchmark in milliseconds; defaults to the sequence candidate benchmark timeout.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 509

def indexesCandidatesBenchmark(
  namespace:,
  max_hits: nil,
  max_object_bytes_per_query: nil,
  max_object_reads_per_query: nil,
  min_recall_at_k: nil,
  min_top_hit_identity: nil,
  queries_object_id: nil,
  queries_path: nil,
  query_mode: nil,
  require_top_hit_id_matches_query_id: nil,
  require_zero_materialization: nil,
  store_artifact: nil,
  timeout_ms: nil,
  request_options: {}
)
  body = {
    'max_hits' => max_hits,
    'max_object_bytes_per_query' => max_object_bytes_per_query,
    'max_object_reads_per_query' => max_object_reads_per_query,
    'min_recall_at_k' => min_recall_at_k,
    'min_top_hit_identity' => min_top_hit_identity,
    'namespace' => namespace,
    'queries_object_id' => queries_object_id,
    'queries_path' => queries_path,
    'query_mode' => query_mode,
    'require_top_hit_id_matches_query_id' => require_top_hit_id_matches_query_id,
    'require_zero_materialization' => require_zero_materialization,
    'store_artifact' => store_artifact,
    'timeout_ms' => timeout_ms
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/candidates/benchmark',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSequenceCandidateBenchmarkData.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

#indexesCandidatesBuild(build_policy: nil, dataset_name: nil, dataset_version: nil, input_object_id: nil, input_path: nil, kmer_size: nil, minimizer_window: nil, name: nil, namespace: nil, payload_shard_records: nil, reduced_alphabet: nil, timeout_ms: nil, version: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSequenceCandidateBuildData

POST /v1/sequences/indexes/candidates/build

Parameters:

  • build_policy (Rafflesia::Types::SequenceCandidateBuildRequestBuildPolicy, nil) (defaults to: nil) —

    Immutable publish policy for an existing namespace. Defaults to if_not_exists.

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

    Optional dataset name carried into build provenance.

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

    Optional dataset version carried into build provenance.

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

    Object id containing input FASTA bytes.

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

    Input FASTA path readable by the API server.

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

    k-mer size used by the sequence candidate; defaults to 5.

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

    Minimizer window used by the sequence candidate; 1 means ordinary contiguous k-mers.

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

    Logical seed index name carried into provenance and namespace derivation.

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

    Explicit sequence candidate namespace. Defaults to a deterministic namespace derived from name and version.

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

    Target records per payload shard in the sequence candidate; defaults to the engine default.

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

    Optional reduced alphabet used before seed extraction, for example protein13.

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

    Hard deadline for this build operation in milliseconds; defaults to the sequence candidate build timeout.

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

    Immutable seed index version carried into provenance and namespace derivation.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 568

def indexesCandidatesBuild(
  build_policy: nil,
  dataset_name: nil,
  dataset_version: nil,
  input_object_id: nil,
  input_path: nil,
  kmer_size: nil,
  minimizer_window: nil,
  name: nil,
  namespace: nil,
  payload_shard_records: nil,
  reduced_alphabet: nil,
  timeout_ms: nil,
  version: nil,
  request_options: {}
)
  body = {
    'build_policy' => build_policy,
    'dataset_name' => dataset_name,
    'dataset_version' => dataset_version,
    'input_object_id' => input_object_id,
    'input_path' => input_path,
    'kmer_size' => kmer_size,
    'minimizer_window' => minimizer_window,
    'name' => name,
    'namespace' => namespace,
    'payload_shard_records' => payload_shard_records,
    'reduced_alphabet' => reduced_alphabet,
    'timeout_ms' => timeout_ms,
    'version' => version
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/candidates/build',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSequenceCandidateBuildData.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

#indexesCandidatesGc(namespace:, apply: nil, from_generation: nil, keep_last_generations: nil, max_garbage_keys: nil, min_generation_age_ms: nil, now_unix_ms: nil, timeout_ms: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSequenceCandidateGcPlanData

POST /v1/sequences/indexes/candidates/gc

Parameters:

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

    Delete garbage objects. False is a dry-run plan.

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

    Manifest generation to retain from; 0 lets the engine use its default current-generation behavior.

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

    Retain the N most recent manifest generations. 0 selects the engine default.

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

    Maximum garbage object keys returned in the response. Defaults to 100; 0 returns all keys.

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

    Optional minimum generation age before an otherwise-garbage generation can be deleted. Requires now_unix_ms.

  • namespace (String) —

    Sequence candidate namespace to plan or apply GC for.

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

    Explicit clock used with min_generation_age_ms for deterministic GC plans.

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

    Hard deadline for this GC operation in milliseconds.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 622

def indexesCandidatesGc(
  namespace:,
  apply: nil,
  from_generation: nil,
  keep_last_generations: nil,
  max_garbage_keys: nil,
  min_generation_age_ms: nil,
  now_unix_ms: nil,
  timeout_ms: nil,
  request_options: {}
)
  body = {
    'apply' => apply,
    'from_generation' => from_generation,
    'keep_last_generations' => keep_last_generations,
    'max_garbage_keys' => max_garbage_keys,
    'min_generation_age_ms' => min_generation_age_ms,
    'namespace' => namespace,
    'now_unix_ms' => now_unix_ms,
    'timeout_ms' => timeout_ms
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/candidates/gc',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSequenceCandidateGcPlanData.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

#indexesCandidatesInspect(namespace:, request_options: {}) ⇒ Rafflesia::EnvelopeSequenceCandidateInspectData

POST /v1/sequences/indexes/candidates/inspect

Parameters:

  • namespace (String) —

    Sequence candidate namespace to inspect.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 659

def indexesCandidatesInspect(
  namespace:,
  request_options: {}
)
  body = {
    'namespace' => namespace
  }
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/candidates/inspect',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSequenceCandidateInspectData.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

#indexesCandidatesSweep(case_timeout_ms: nil, dataset_name: nil, dataset_version: nil, input_object_id: nil, input_path: nil, kmer_sizes: nil, max_hits: nil, max_object_bytes_per_query: nil, max_object_reads_per_query: nil, min_recall_at_k: nil, minimizer_windows: nil, name: nil, namespace_prefix: nil, payload_shard_records: nil, publish_selected_namespace: nil, queries_object_id: nil, queries_path: nil, query_modes: nil, reduced_alphabets: nil, require_zero_materialization: nil, store_artifact: nil, timeout_ms: nil, version: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSequenceCandidateSweepData

POST /v1/sequences/indexes/candidates/sweep

Parameters:

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

    Hard deadline per candidate layout build/measurement case in milliseconds; defaults to the sequence candidate case timeout.

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

    Optional dataset name carried into scratch build provenance.

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

    Optional dataset version carried into scratch build provenance.

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

    Object id containing input FASTA bytes.

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

    Input FASTA path readable by the API server.

  • kmer_sizes (Array<Integer>, nil) (defaults to: nil) —

    k-mer sizes to sweep. Defaults to [3,4,5].

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

    Maximum hits per query; defaults to 10.

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

    Optional feasibility threshold for mean object bytes fetched per query.

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

    Optional feasibility threshold for mean object reads per query.

  • min_recall_at_k (Float, nil) (defaults to: nil) —

    Feasibility threshold for mean recall@k. Defaults to 0.99.

  • minimizer_windows (Array<Integer>, nil) (defaults to: nil) —

    Minimizer windows to sweep. Defaults to [1,4].

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

    Logical seed index name carried into scratch namespace derivation and provenance.

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

    Optional scratch namespace prefix. Defaults to a deterministic prefix derived from name/version/source/query hashes.

  • payload_shard_records (Array<Integer>, nil) (defaults to: nil) —

    Payload shard record targets to sweep. Defaults to [64,256].

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

    Optional canonical namespace to build with the selected layout after the sweep completes.

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

    Object id containing benchmark query FASTA bytes.

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

    Multi-record FASTA path containing benchmark queries.

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

    Query modes to sweep. Defaults to [bounded_fast,exact_safe].

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

    Reduced alphabets to sweep. Empty string means identity alphabet.

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

    Require every measured query to report zero materialized database bytes.

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

    Whether to store the sweep JSON artifact in the object store; defaults to true.

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

    Hard deadline for the whole sweep in milliseconds; defaults to the sequence candidate sweep timeout.

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

    Logical seed index version carried into scratch namespace derivation and provenance.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 704

def indexesCandidatesSweep(
  case_timeout_ms: nil,
  dataset_name: nil,
  dataset_version: nil,
  input_object_id: nil,
  input_path: nil,
  kmer_sizes: nil,
  max_hits: nil,
  max_object_bytes_per_query: nil,
  max_object_reads_per_query: nil,
  min_recall_at_k: nil,
  minimizer_windows: nil,
  name: nil,
  namespace_prefix: nil,
  payload_shard_records: nil,
  publish_selected_namespace: nil,
  queries_object_id: nil,
  queries_path: nil,
  query_modes: nil,
  reduced_alphabets: nil,
  require_zero_materialization: nil,
  store_artifact: nil,
  timeout_ms: nil,
  version: nil,
  request_options: {}
)
  body = {
    'case_timeout_ms' => case_timeout_ms,
    'dataset_name' => dataset_name,
    'dataset_version' => dataset_version,
    'input_object_id' => input_object_id,
    'input_path' => input_path,
    'kmer_sizes' => kmer_sizes,
    'max_hits' => max_hits,
    'max_object_bytes_per_query' => max_object_bytes_per_query,
    'max_object_reads_per_query' => max_object_reads_per_query,
    'min_recall_at_k' => min_recall_at_k,
    'minimizer_windows' => minimizer_windows,
    'name' => name,
    'namespace_prefix' => namespace_prefix,
    'payload_shard_records' => payload_shard_records,
    'publish_selected_namespace' => publish_selected_namespace,
    'queries_object_id' => queries_object_id,
    'queries_path' => queries_path,
    'query_modes' => query_modes,
    'reduced_alphabets' => reduced_alphabets,
    'require_zero_materialization' => require_zero_materialization,
    'store_artifact' => store_artifact,
    'timeout_ms' => timeout_ms,
    'version' => version
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/candidates/sweep',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSequenceCandidateSweepData.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

#indexesCandidatesVerify(namespace:, check_gc_plan: nil, expected_source_sha_256: nil, max_gc_garbage_count: nil, max_object_bytes: nil, max_object_reads: nil, min_record_count: nil, min_top_hit_identity: nil, probe_max_hits: nil, probe_query: nil, require_payload_shards: nil, require_posting_segment: nil, require_probe_hit: nil, require_zero_materialization: nil, timeout_ms: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSequenceCandidateVerifyData

POST /v1/sequences/indexes/candidates/verify

Parameters:

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

    Also compute a dry-run GC plan.

  • expected_source_sha_256 (String, nil) (defaults to: nil) —

    Optional source SHA-256 that the namespace must advertise.

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

    Optional maximum dry-run garbage object count when check_gc_plan is true. Set 0 to require no garbage objects.

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

    Optional object-byte budget for the probe query.

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

    Optional object-read budget for the probe query.

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

    Optional minimum indexed record count.

  • min_top_hit_identity (Float, nil) (defaults to: nil) —

    Optional minimum identity for the probe top hit.

  • namespace (String) —

    Sequence candidate namespace to verify.

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

    Maximum probe hits; defaults to 1.

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

    Optional query sequence, sequence id, or FASTA path to probe with the index.

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

    Require the directory to expose at least one payload shard.

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

    Require the directory to expose a posting segment object.

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

    Require the optional probe query to return at least one hit.

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

    Require optional probe query to report zero materialized database bytes.

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

    Hard deadline for this verification in milliseconds.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 785

def indexesCandidatesVerify(
  namespace:,
  check_gc_plan: nil,
  expected_source_sha_256: nil,
  max_gc_garbage_count: nil,
  max_object_bytes: nil,
  max_object_reads: nil,
  min_record_count: nil,
  min_top_hit_identity: nil,
  probe_max_hits: nil,
  probe_query: nil,
  require_payload_shards: nil,
  require_posting_segment: nil,
  require_probe_hit: nil,
  require_zero_materialization: nil,
  timeout_ms: nil,
  request_options: {}
)
  body = {
    'check_gc_plan' => check_gc_plan,
    'expected_source_sha256' => expected_source_sha_256,
    'max_gc_garbage_count' => max_gc_garbage_count,
    'max_object_bytes' => max_object_bytes,
    'max_object_reads' => max_object_reads,
    'min_record_count' => min_record_count,
    'min_top_hit_identity' => min_top_hit_identity,
    'namespace' => namespace,
    'probe_max_hits' => probe_max_hits,
    'probe_query' => probe_query,
    'require_payload_shards' => require_payload_shards,
    'require_posting_segment' => require_posting_segment,
    'require_probe_hit' => require_probe_hit,
    'require_zero_materialization' => require_zero_materialization,
    'timeout_ms' => timeout_ms
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/candidates/verify',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSequenceCandidateVerifyData.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

#indexesDiamondBuild(name:, version:, dry_run: nil, extra_args: nil, input_file_name: nil, input_object_id: nil, input_path: nil, output_dir: nil, register_manifest: nil, store_artifacts: nil, threads: nil, request_options: {}) ⇒ Rafflesia::EnvelopeDiamondDbBuildData

POST /v1/sequences/indexes/diamond/build

Parameters:

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

    Return the deterministic plan without executing diamond makedb

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

    Explicit additional diamond makedb arguments

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

    Optional filename to use when materializing input_object_id

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

    Object id for an input protein FASTA artifact

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

    Input protein FASTA path

  • name (String) —

    Logical database name, for example uniprot_swissprot

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

    Directory for generated DIAMOND DB files and manifest

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

    Whether to publish the manifest into the local DIAMOND DB registry after build

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

    Whether to store generated artifacts in the object store; defaults to true

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

    DIAMOND makedb thread count

  • version (String) —

    Immutable logical database version

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 846

def indexesDiamondBuild(
  name:,
  version:,
  dry_run: nil,
  extra_args: nil,
  input_file_name: nil,
  input_object_id: nil,
  input_path: nil,
  output_dir: nil,
  register_manifest: nil,
  store_artifacts: nil,
  threads: nil,
  request_options: {}
)
  body = {
    'dry_run' => dry_run,
    'extra_args' => extra_args,
    'input_file_name' => input_file_name,
    'input_object_id' => input_object_id,
    'input_path' => input_path,
    'name' => name,
    'output_dir' => output_dir,
    'register_manifest' => register_manifest,
    'store_artifacts' => store_artifacts,
    'threads' => threads,
    'version' => version
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/diamond/build',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeDiamondDbBuildData.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

#indexesDiamondCatalogBuild(name:, version:, catalog: nil, dry_run: nil, extra_args: nil, input_file_name: nil, input_object_id: nil, input_path: nil, output_dir: nil, shard_count: nil, store_root: nil, threads: nil, request_options: {}) ⇒ Rafflesia::EnvelopeDiamondCatalogBuildData

POST /v1/sequences/indexes/diamond/catalog/build

Parameters:

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

    Object key for the catalog JSON; defaults to catalogs/name/version/diamond-catalog.json

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

    Return the deterministic sharded build plan without executing diamond makedb

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

    Explicit additional diamond makedb arguments

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

    Optional filename to use when materializing input_object_id

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

    Object id for an input protein FASTA artifact

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

    Input protein FASTA path

  • name (String) —

    Logical catalog name, for example uniprot_swissprot

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

    Directory for temporary shard FASTA and DIAMOND DB build files

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

    Requested number of FASTA shards; defaults to 1 and is capped at the number of records

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

    Object-store root for the catalog and shard databases; defaults to the server data dir

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

    DIAMOND makedb thread count per shard

  • version (String) —

    Immutable logical catalog version

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 900

def indexesDiamondCatalogBuild(
  name:,
  version:,
  catalog: nil,
  dry_run: nil,
  extra_args: nil,
  input_file_name: nil,
  input_object_id: nil,
  input_path: nil,
  output_dir: nil,
  shard_count: nil,
  store_root: nil,
  threads: nil,
  request_options: {}
)
  body = {
    'catalog' => catalog,
    'dry_run' => dry_run,
    'extra_args' => extra_args,
    'input_file_name' => input_file_name,
    'input_object_id' => input_object_id,
    'input_path' => input_path,
    'name' => name,
    'output_dir' => output_dir,
    'shard_count' => shard_count,
    'store_root' => store_root,
    'threads' => threads,
    'version' => version
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/diamond/catalog/build',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeDiamondCatalogBuildData.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

#indexesDiamondDescribe(manifest_path: nil, ref: nil, request_options: {}) ⇒ Rafflesia::EnvelopeDiamondDbDescribeData

POST /v1/sequences/indexes/diamond/describe

Parameters:

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

    Local manifest path

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

    Published DB ref such as name:version or manifest object id

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 946

def indexesDiamondDescribe(
  manifest_path: nil,
  ref: nil,
  request_options: {}
)
  body = {
    'manifest_path' => manifest_path,
    'ref' => ref
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/diamond/describe',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeDiamondDbDescribeData.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

#indexesDiamondEvict(dry_run: nil, manifest_path: nil, max_bytes: nil, policy: nil, ref: nil, target_dir: nil, request_options: {}) ⇒ Rafflesia::EnvelopeDiamondDbEvictData

POST /v1/sequences/indexes/diamond/evict

Parameters:

  • dry_run (Boolean, nil) (defaults to: nil)
  • manifest_path (String, nil) (defaults to: nil)
  • max_bytes (Integer, nil) (defaults to: nil) —

    If positive, evict oldest selected cache files until selected cache bytes are at or below this limit. Zero evicts every selected file.

  • policy (Rafflesia::CacheEvictionPolicy, nil) (defaults to: nil) —

    Optional cache policy for TTL and pinned-path eviction controls.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 976

def indexesDiamondEvict(
  dry_run: nil,
  manifest_path: nil,
  max_bytes: nil,
  policy: nil,
  ref: nil,
  target_dir: nil,
  request_options: {}
)
  body = {
    'dry_run' => dry_run,
    'manifest_path' => manifest_path,
    'max_bytes' => max_bytes,
    'policy' => policy,
    'ref' => ref,
    'target_dir' => target_dir
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/diamond/evict',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeDiamondDbEvictData.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

#indexesDiamondList(limit: nil, request_options: {}) ⇒ Rafflesia::EnvelopeDiamondDbListData

GET /v1/sequences/indexes/diamond/list

Parameters:

  • limit (Integer, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 1009

def indexesDiamondList(
  limit: nil,
  request_options: {}
)
  params = {
    'limit' => limit
  }.compact
  response = @client.request(
    method: :get,
    path: '/v1/sequences/indexes/diamond/list',
    auth: true,
    params: params,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeDiamondDbListData.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

#indexesDiamondMaterialize(manifest_path: nil, ref: nil, target_dir: nil, verify: nil, request_options: {}) ⇒ Rafflesia::EnvelopeDiamondDbMaterializeData

POST /v1/sequences/indexes/diamond/materialize

Parameters:

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

    Local manifest path

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

    Published DB ref such as name:version or manifest object id

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

    Directory used as the local DIAMOND DB cache

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

    Verify materialized files by SHA-256

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 1035

def indexesDiamondMaterialize(
  manifest_path: nil,
  ref: nil,
  target_dir: nil,
  verify: nil,
  request_options: {}
)
  body = {
    'manifest_path' => manifest_path,
    'ref' => ref,
    'target_dir' => target_dir,
    'verify' => verify
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/diamond/materialize',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeDiamondDbMaterializeData.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

#indexesDiamondPublish(manifest_object_id: nil, manifest_path: nil, ref: nil, request_options: {}) ⇒ Rafflesia::EnvelopeDiamondDbPublishData

POST /v1/sequences/indexes/diamond/publish

Parameters:

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

    Manifest object id

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

    Local manifest path

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

    Published DB ref override

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 1066

def indexesDiamondPublish(
  manifest_object_id: nil,
  manifest_path: nil,
  ref: nil,
  request_options: {}
)
  body = {
    'manifest_object_id' => manifest_object_id,
    'manifest_path' => manifest_path,
    'ref' => ref
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/diamond/publish',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeDiamondDbPublishData.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

#indexesDiamondVerify(manifest_path: nil, ref: nil, target_dir: nil, request_options: {}) ⇒ Rafflesia::EnvelopeDiamondDbVerifyData

POST /v1/sequences/indexes/diamond/verify

Parameters:

  • manifest_path (String, nil) (defaults to: nil)
  • ref (String, nil) (defaults to: nil)
  • target_dir (String, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 1095

def indexesDiamondVerify(
  manifest_path: nil,
  ref: nil,
  target_dir: nil,
  request_options: {}
)
  body = {
    'manifest_path' => manifest_path,
    'ref' => ref,
    'target_dir' => target_dir
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/diamond/verify',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeDiamondDbVerifyData.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

#indexesSeedBenchmark(queries_path:, concurrency: nil, db: nil, index_id: nil, input_object_id: nil, input_path: nil, kmer_size: nil, manifest_object_id: nil, manifest_path: nil, max_hits: nil, max_object_bytes_per_query: nil, max_object_reads_per_query: nil, min_identity: nil, min_mean_overlap_fraction: nil, name: nil, payload_block_size: nil, posting_block_size: nil, require_zero_materialization: nil, rerank_alignment: nil, store_artifact: nil, use_block_cache: nil, version: nil, wal_object_ids: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSequenceSeedIndexBenchmarkData

POST /v1/sequences/indexes/seed/benchmark

Parameters:

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

    Maximum concurrent object block reads; defaults to 8

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

    Baseline FASTA path for the materialized builtin k-mer search; defaults to input_path when available

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

    Published sequence seed index id

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

    Object id containing input FASTA bytes used to build a seed index when no manifest is supplied

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

    Input FASTA path used to build a seed index when no manifest is supplied

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

    k-mer size used for build/search; defaults to the index k-mer size or 9

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

    Object id for an existing sequence seed index manifest

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

    Local path to an existing sequence seed index manifest JSON file

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

    Maximum hits per query; defaults to 100

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

    Optional pass threshold for object bytes fetched per query

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

    Optional pass threshold for object reads per query

  • min_identity (Float, nil) (defaults to: nil) —

    Minimum k-mer identity fraction for both search paths

  • min_mean_overlap_fraction (Float, nil) (defaults to: nil) —

    Optional pass threshold for mean hit-overlap fraction

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

    Logical seed index name when building an index for the benchmark

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

    Payload block size when building an index for the benchmark

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

    Posting block size when building an index for the benchmark

  • queries_path (String) —

    Multi-record FASTA path containing benchmark queries

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

    Require the object-native search path to report zero materialized database bytes

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

    Whether seed-index candidate hits are alignment-reranked before comparison

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

    Whether to store the benchmark JSON artifact in the object store; defaults to true

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

    Whether to use the process-local seed-index object block cache; defaults to true

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

    Logical seed index version when building an index for the benchmark

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

    Optional WAL object ids to overlay on the immutable index during benchmark queries

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 1144

def indexesSeedBenchmark(
  queries_path:,
  concurrency: nil,
  db: nil,
  index_id: nil,
  input_object_id: nil,
  input_path: nil,
  kmer_size: nil,
  manifest_object_id: nil,
  manifest_path: nil,
  max_hits: nil,
  max_object_bytes_per_query: nil,
  max_object_reads_per_query: nil,
  min_identity: nil,
  min_mean_overlap_fraction: nil,
  name: nil,
  payload_block_size: nil,
  posting_block_size: nil,
  require_zero_materialization: nil,
  rerank_alignment: nil,
  store_artifact: nil,
  use_block_cache: nil,
  version: nil,
  wal_object_ids: nil,
  request_options: {}
)
  body = {
    'concurrency' => concurrency,
    'db' => db,
    'index_id' => index_id,
    'input_object_id' => input_object_id,
    'input_path' => input_path,
    'kmer_size' => kmer_size,
    'manifest_object_id' => manifest_object_id,
    'manifest_path' => manifest_path,
    'max_hits' => max_hits,
    'max_object_bytes_per_query' => max_object_bytes_per_query,
    'max_object_reads_per_query' => max_object_reads_per_query,
    'min_identity' => min_identity,
    'min_mean_overlap_fraction' => min_mean_overlap_fraction,
    'name' => name,
    'payload_block_size' => payload_block_size,
    'posting_block_size' => posting_block_size,
    'queries_path' => queries_path,
    'require_zero_materialization' => require_zero_materialization,
    'rerank_alignment' => rerank_alignment,
    'store_artifact' => store_artifact,
    'use_block_cache' => use_block_cache,
    'version' => version,
    'wal_object_ids' => wal_object_ids
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/seed/benchmark',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSequenceSeedIndexBenchmarkData.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

#indexesSeedBuild(name:, version:, dataset_name: nil, dataset_version: nil, input_object_id: nil, input_path: nil, kmer_size: nil, payload_block_size: nil, payload_lite: nil, posting_block_size: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSequenceSeedIndexBuildData

POST /v1/sequences/indexes/seed/build

Parameters:

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

    Optional dataset name carried into index provenance

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

    Optional dataset version carried into index provenance

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

    Object id containing input FASTA bytes

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

    Input FASTA path

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

    k-mer size used to build the seed posting lists; defaults to 9

  • name (String) —

    Logical seed index name, for example uniprot_swissprot_seed

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

    Maximum sequence payload records stored in one payload block; defaults to 1024

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

    When true, payload blocks omit full subject sequences and store only routing metadata; exact scoring must use an authoritative sequence store such as BLAST pack segments.

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

    Maximum postings stored in one posting-list block; defaults to 4096

  • version (String) —

    Immutable seed index version or source snapshot

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 1220

def indexesSeedBuild(
  name:,
  version:,
  dataset_name: nil,
  dataset_version: nil,
  input_object_id: nil,
  input_path: nil,
  kmer_size: nil,
  payload_block_size: nil,
  payload_lite: nil,
  posting_block_size: nil,
  request_options: {}
)
  body = {
    'dataset_name' => dataset_name,
    'dataset_version' => dataset_version,
    'input_object_id' => input_object_id,
    'input_path' => input_path,
    'kmer_size' => kmer_size,
    'name' => name,
    'payload_block_size' => payload_block_size,
    'payload_lite' => payload_lite,
    'posting_block_size' => posting_block_size,
    'version' => version
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/seed/build',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSequenceSeedIndexBuildData.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

#indexesSeedCompact(name:, version:, base_index_id: nil, base_manifest_object_id: nil, base_manifest_path: nil, base_name: nil, base_version: nil, dataset_name: nil, dataset_version: nil, kmer_size: nil, payload_block_size: nil, posting_block_size: nil, wal_object_ids: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSequenceSeedIndexCompactData

POST /v1/sequences/indexes/seed/compact

Parameters:

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

    Published base sequence seed index id

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

    Object id for the base sequence seed index manifest

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

    Local path to the base sequence seed index manifest JSON file

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

    Published base seed index name

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

    Published base seed index version

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

    Optional dataset name carried into compacted index provenance

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

    Optional dataset version carried into compacted index provenance

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

    Optional compacted k-mer size; defaults to the base index k-mer size

  • name (String) —

    Logical name for the compacted seed index

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

    Payload block size for the compacted index

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

    Posting block size for the compacted index

  • version (String) —

    Immutable version for the compacted seed index

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

    WAL object ids to compact into the new immutable seed index

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 1273

def indexesSeedCompact(
  name:,
  version:,
  base_index_id: nil,
  base_manifest_object_id: nil,
  base_manifest_path: nil,
  base_name: nil,
  base_version: nil,
  dataset_name: nil,
  dataset_version: nil,
  kmer_size: nil,
  payload_block_size: nil,
  posting_block_size: nil,
  wal_object_ids: nil,
  request_options: {}
)
  body = {
    'base_index_id' => base_index_id,
    'base_manifest_object_id' => base_manifest_object_id,
    'base_manifest_path' => base_manifest_path,
    'base_name' => base_name,
    'base_version' => base_version,
    'dataset_name' => dataset_name,
    'dataset_version' => dataset_version,
    'kmer_size' => kmer_size,
    'name' => name,
    'payload_block_size' => payload_block_size,
    'posting_block_size' => posting_block_size,
    'version' => version,
    'wal_object_ids' => wal_object_ids
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/seed/compact',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSequenceSeedIndexCompactData.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

#indexesSeedDescribe(index_id: nil, manifest_object_id: nil, manifest_path: nil, name: nil, version: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSequenceSeedIndexInspectData

POST /v1/sequences/indexes/seed/describe

Parameters:

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

    Published sequence seed index id

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

    Object id for a sequence seed index manifest

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

    Local path to a sequence seed index manifest JSON file

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

    Published sequence seed index name

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

    Published sequence seed index version

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 1324

def indexesSeedDescribe(
  index_id: nil,
  manifest_object_id: nil,
  manifest_path: nil,
  name: nil,
  version: nil,
  request_options: {}
)
  body = {
    'index_id' => index_id,
    'manifest_object_id' => manifest_object_id,
    'manifest_path' => manifest_path,
    'name' => name,
    'version' => version
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/seed/describe',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSequenceSeedIndexInspectData.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

#indexesSeedList(name: nil, version: nil, limit: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSequenceSeedIndexListData

GET /v1/sequences/indexes/seed/list

Parameters:

  • name (String, nil) (defaults to: nil)
  • version (String, nil) (defaults to: nil)
  • limit (Integer, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 1357

def indexesSeedList(
  name: nil,
  version: nil,
  limit: nil,
  request_options: {}
)
  params = {
    'name' => name,
    'version' => version,
    'limit' => limit
  }.compact
  response = @client.request(
    method: :get,
    path: '/v1/sequences/indexes/seed/list',
    auth: true,
    params: params,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSequenceSeedIndexListData.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

#indexesSeedMerge(name:, segment_manifest_object_ids:, version:, dataset_name: nil, dataset_version: nil, kmer_size: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSequenceSeedIndexMergeData

POST /v1/sequences/indexes/seed/merge

Parameters:

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

    Optional dataset name carried into aggregate index provenance

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

    Optional dataset version carried into aggregate index provenance

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

    Optional k-mer size guard; every segment must match when set

  • name (String) —

    Logical name for the aggregate seed index

  • segment_manifest_object_ids (Array<String>, nil) —

    Seed index manifest object ids to publish as immutable query segments

  • version (String) —

    Immutable version for the aggregate seed index

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 1389

def indexesSeedMerge(
  name:,
  segment_manifest_object_ids:,
  version:,
  dataset_name: nil,
  dataset_version: nil,
  kmer_size: nil,
  request_options: {}
)
  body = {
    'dataset_name' => dataset_name,
    'dataset_version' => dataset_version,
    'kmer_size' => kmer_size,
    'name' => name,
    'segment_manifest_object_ids' => segment_manifest_object_ids,
    'version' => version
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/seed/merge',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSequenceSeedIndexMergeData.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

#indexesSeedPlan(query:, index_id: nil, kmer_size: nil, manifest_object_id: nil, manifest_path: nil, max_object_bytes: nil, max_object_reads: nil, name: nil, require_zero_materialization: nil, version: nil, wal_object_ids: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSequenceSeedIndexPlanData

POST /v1/sequences/indexes/seed/plan

Parameters:

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

    Published sequence seed index id

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

    Optional query k-mer size; must match the index k-mer size when set

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

    Object id for a sequence seed index manifest

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

    Local path to a sequence seed index manifest JSON file

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

    Optional object-byte budget checked against the plan

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

    Optional object-read budget checked against the plan

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

    Published sequence seed index name

  • query (String) —

    Sequence ID or local FASTA path for query sequence

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

    Require the planned object-native path to materialize zero database bytes

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

    Published sequence seed index version

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

    Optional WAL object ids included as a mutable overlay during planning

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 1432

def indexesSeedPlan(
  query:,
  index_id: nil,
  kmer_size: nil,
  manifest_object_id: nil,
  manifest_path: nil,
  max_object_bytes: nil,
  max_object_reads: nil,
  name: nil,
  require_zero_materialization: nil,
  version: nil,
  wal_object_ids: nil,
  request_options: {}
)
  body = {
    'index_id' => index_id,
    'kmer_size' => kmer_size,
    'manifest_object_id' => manifest_object_id,
    'manifest_path' => manifest_path,
    'max_object_bytes' => max_object_bytes,
    'max_object_reads' => max_object_reads,
    'name' => name,
    'query' => query,
    'require_zero_materialization' => require_zero_materialization,
    'version' => version,
    'wal_object_ids' => wal_object_ids
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/seed/plan',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSequenceSeedIndexPlanData.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

#indexesSeedPublish(benchmark_object_id: nil, manifest_object_id: nil, manifest_path: nil, max_object_bytes_per_query: nil, max_object_reads_per_query: nil, min_mean_overlap_fraction: nil, require_benchmark: nil, require_zero_materialization: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSequenceSeedIndexInspectData

POST /v1/sequences/indexes/seed/publish

Parameters:

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

    Object id of a sequence seed-index benchmark artifact produced by sequences.indexes.seed.benchmark

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

    Object id for a sequence seed index manifest

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

    Local path to a sequence seed index manifest JSON file

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

    Optional publish gate threshold for object bytes fetched per query

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

    Optional publish gate threshold for object reads per query

  • min_mean_overlap_fraction (Float, nil) (defaults to: nil) —

    Optional publish gate threshold for mean hit-overlap fraction against the materialized FASTA baseline

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

    Require a passing object-native seed-index benchmark artifact before publishing

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

    Require benchmark evidence that the object-native path materialized zero database bytes

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 1482

def indexesSeedPublish(
  benchmark_object_id: nil,
  manifest_object_id: nil,
  manifest_path: nil,
  max_object_bytes_per_query: nil,
  max_object_reads_per_query: nil,
  min_mean_overlap_fraction: nil,
  require_benchmark: nil,
  require_zero_materialization: nil,
  request_options: {}
)
  body = {
    'benchmark_object_id' => benchmark_object_id,
    'manifest_object_id' => manifest_object_id,
    'manifest_path' => manifest_path,
    'max_object_bytes_per_query' => max_object_bytes_per_query,
    'max_object_reads_per_query' => max_object_reads_per_query,
    'min_mean_overlap_fraction' => min_mean_overlap_fraction,
    'require_benchmark' => require_benchmark,
    'require_zero_materialization' => require_zero_materialization
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/seed/publish',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSequenceSeedIndexInspectData.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

#indexesSeedVerify(check_blocks: nil, index_id: nil, manifest_object_id: nil, manifest_path: nil, name: nil, version: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSequenceSeedIndexVerifyData

POST /v1/sequences/indexes/seed/verify

Parameters:

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

    When true, read every posting and payload block; otherwise verifies manifest and directory objects

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

    Published sequence seed index id

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

    Object id for a sequence seed index manifest

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

    Local path to a sequence seed index manifest JSON file

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

    Published sequence seed index name

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

    Published sequence seed index version

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 1524

def indexesSeedVerify(
  check_blocks: nil,
  index_id: nil,
  manifest_object_id: nil,
  manifest_path: nil,
  name: nil,
  version: nil,
  request_options: {}
)
  body = {
    'check_blocks' => check_blocks,
    'index_id' => index_id,
    'manifest_object_id' => manifest_object_id,
    'manifest_path' => manifest_path,
    'name' => name,
    'version' => version
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/seed/verify',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSequenceSeedIndexVerifyData.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

#indexesSeedWalAppend(index_id: nil, input_object_id: nil, input_path: nil, manifest_object_id: nil, manifest_path: nil, name: nil, records: nil, version: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSequenceSeedIndexWalAppendData

POST /v1/sequences/indexes/seed/wal/append

Parameters:

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

    Published base sequence seed index id

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

    Optional FASTA object whose records become upsert WAL records

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

    Optional FASTA file whose records become upsert WAL records

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

    Object id for the base sequence seed index manifest

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

    Local path to the base sequence seed index manifest JSON file

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

    Published base seed index name or WAL name when no base locator is supplied

  • records (Array<Rafflesia::SequenceSeedIndexWalRecord>, nil) (defaults to: nil) —

    Explicit WAL records

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

    Published base seed index version or WAL version when no base locator is supplied

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 1564

def indexesSeedWalAppend(
  index_id: nil,
  input_object_id: nil,
  input_path: nil,
  manifest_object_id: nil,
  manifest_path: nil,
  name: nil,
  records: nil,
  version: nil,
  request_options: {}
)
  body = {
    'index_id' => index_id,
    'input_object_id' => input_object_id,
    'input_path' => input_path,
    'manifest_object_id' => manifest_object_id,
    'manifest_path' => manifest_path,
    'name' => name,
    'records' => records,
    'version' => version
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/seed/wal/append',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSequenceSeedIndexWalAppendData.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

#indexesSegmentsBuild(algorithm:, name:, version:, block_size_bytes: nil, dataset_name: nil, dataset_version: nil, input_object_id: nil, input_path: nil, key_mode: nil, tool_name: nil, tool_version: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSearchSegmentBuildData

POST /v1/sequences/indexes/segments/build

Parameters:

  • algorithm (String) —

    Algorithm family that owns this segment layout, for example blast, foldseek, or seed.

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

    Maximum bytes per immutable block; defaults to 4 MiB.

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

    Optional dataset name carried into segment provenance.

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

    Optional dataset version carried into segment provenance.

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

    Object id containing input bytes to split into immutable segment blocks.

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

    Input file path whose bytes will be split into immutable segment blocks.

  • key_mode (Rafflesia::Types::SearchSegmentBuildRequestKeyMode, nil) (defaults to: nil) —

    Sparse-index key mode; line uses the first non-empty line prefix in each block, byte_offset uses deterministic offsets. Defaults to line.

  • name (String) —

    Logical search segment name.

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

    Optional upstream tool name carried into the manifest.

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

    Optional upstream tool version carried into the manifest.

  • version (String) —

    Immutable segment version or source snapshot.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 1611

def indexesSegmentsBuild(
  algorithm:,
  name:,
  version:,
  block_size_bytes: nil,
  dataset_name: nil,
  dataset_version: nil,
  input_object_id: nil,
  input_path: nil,
  key_mode: nil,
  tool_name: nil,
  tool_version: nil,
  request_options: {}
)
  body = {
    'algorithm' => algorithm,
    'block_size_bytes' => block_size_bytes,
    'dataset_name' => dataset_name,
    'dataset_version' => dataset_version,
    'input_object_id' => input_object_id,
    'input_path' => input_path,
    'key_mode' => key_mode,
    'name' => name,
    'tool_name' => tool_name,
    'tool_version' => tool_version,
    'version' => version
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/segments/build',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSearchSegmentBuildData.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

#indexesSegmentsDescribe(manifest_object_id: nil, manifest_path: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSearchSegmentDescribeData

POST /v1/sequences/indexes/segments/describe

Parameters:

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

    Object id for a search segment manifest.

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

    Local path to a search segment manifest JSON file.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 1655

def indexesSegmentsDescribe(
  manifest_object_id: nil,
  manifest_path: nil,
  request_options: {}
)
  body = {
    'manifest_object_id' => manifest_object_id,
    'manifest_path' => manifest_path
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/segments/describe',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSearchSegmentDescribeData.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

#indexesSegmentsGc(candidate_manifest_object_ids: nil, candidate_manifest_paths: nil, dry_run: nil, keep_manifest_object_ids: nil, keep_manifest_paths: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSearchSegmentGcData

POST /v1/sequences/indexes/segments/gc

Parameters:

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

    Older/candidate manifest object ids considered for garbage collection.

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

    Older/candidate manifest paths considered for garbage collection.

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

    When true, compute unused object ids without deleting. Defaults to true because deletion is not exposed by the content-addressed store.

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

    Manifest object ids whose block/root/source objects remain live.

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

    Local manifest paths whose block/root/source objects remain live.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 1684

def indexesSegmentsGc(
  candidate_manifest_object_ids: nil,
  candidate_manifest_paths: nil,
  dry_run: nil,
  keep_manifest_object_ids: nil,
  keep_manifest_paths: nil,
  request_options: {}
)
  body = {
    'candidate_manifest_object_ids' => candidate_manifest_object_ids,
    'candidate_manifest_paths' => candidate_manifest_paths,
    'dry_run' => dry_run,
    'keep_manifest_object_ids' => keep_manifest_object_ids,
    'keep_manifest_paths' => keep_manifest_paths
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/segments/gc',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSearchSegmentGcData.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

#indexesSegmentsPlan(manifest_object_id: nil, manifest_path: nil, max_blocks: nil, max_materialized_bytes: nil, max_object_bytes: nil, max_object_reads: nil, query_key: nil, require_zero_materialization: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSearchSegmentPlanData

POST /v1/sequences/indexes/segments/plan

Parameters:

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

    Object id for a search segment manifest.

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

    Local path to a search segment manifest JSON file.

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

    Optional hard budget for selected immutable blocks.

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

    Optional hard budget for planned database/local materialization bytes.

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

    Optional hard budget for planned object bytes.

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

    Optional hard budget for planned object reads.

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

    Sparse-index key used to select block objects. Empty plans every block.

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

    Require the plan to materialize zero database/local bytes.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 1722

def indexesSegmentsPlan(
  manifest_object_id: nil,
  manifest_path: nil,
  max_blocks: nil,
  max_materialized_bytes: nil,
  max_object_bytes: nil,
  max_object_reads: nil,
  query_key: nil,
  require_zero_materialization: nil,
  request_options: {}
)
  body = {
    'manifest_object_id' => manifest_object_id,
    'manifest_path' => manifest_path,
    'max_blocks' => max_blocks,
    'max_materialized_bytes' => max_materialized_bytes,
    'max_object_bytes' => max_object_bytes,
    'max_object_reads' => max_object_reads,
    'query_key' => query_key,
    'require_zero_materialization' => require_zero_materialization
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/segments/plan',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSearchSegmentPlanData.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

#indexesSegmentsPrefetch(manifest_object_id: nil, manifest_path: nil, max_materialized_bytes: nil, max_object_bytes: nil, max_object_reads: nil, query_key: nil, require_zero_materialization: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSearchSegmentPrefetchData

POST /v1/sequences/indexes/segments/prefetch

Parameters:

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

    Object id for a search segment manifest.

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

    Local path to a search segment manifest JSON file.

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

    Optional hard budget for planned database/local materialization bytes.

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

    Optional hard budget for planned object bytes.

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

    Optional hard budget for planned object reads.

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

    Sparse-index key used to select block objects. Empty prefetches every block.

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

    Require the prefetch path to materialize zero database/local bytes.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 1765

def indexesSegmentsPrefetch(
  manifest_object_id: nil,
  manifest_path: nil,
  max_materialized_bytes: nil,
  max_object_bytes: nil,
  max_object_reads: nil,
  query_key: nil,
  require_zero_materialization: nil,
  request_options: {}
)
  body = {
    'manifest_object_id' => manifest_object_id,
    'manifest_path' => manifest_path,
    'max_materialized_bytes' => max_materialized_bytes,
    'max_object_bytes' => max_object_bytes,
    'max_object_reads' => max_object_reads,
    'query_key' => query_key,
    'require_zero_materialization' => require_zero_materialization
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/indexes/segments/prefetch',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSearchSegmentPrefetchData.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

#msaBuild(backend: nil, cache_mode: nil, dry_run: nil, extra_args: nil, input_object_id: nil, input_path: nil, inputs: nil, output_dir: nil, strategy: nil, threads: nil, request_options: {}) ⇒ Rafflesia::EnvelopeMsaBuildData

POST /v1/sequences/msa/build

Parameters:

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

    MSA backend; defaults to mafft

  • cache_mode (Rafflesia::Types::MsaBuildRequestCacheMode, nil) (defaults to: nil) —

    Artifact cache mode. use reuses matching cached artifacts, refresh recomputes and stores, off recomputes without storing.

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

    Return the deterministic command without executing the backend

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

    Explicit additional backend arguments

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

    Object id for an input multi-record FASTA artifact

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

    Input multi-record FASTA path

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

    Sequence ids or local FASTA paths to combine into the MSA input

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

    Directory for generated MSA run files

  • strategy (Rafflesia::Types::MsaBuildRequestStrategy, nil) (defaults to: nil) —

    MAFFT strategy; defaults to auto

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

    MAFFT thread count; defaults to 1

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 1809

def msaBuild(
  backend: nil,
  cache_mode: nil,
  dry_run: nil,
  extra_args: nil,
  input_object_id: nil,
  input_path: nil,
  inputs: nil,
  output_dir: nil,
  strategy: nil,
  threads: nil,
  request_options: {}
)
  body = {
    'backend' => backend,
    'cache_mode' => cache_mode,
    'dry_run' => dry_run,
    'extra_args' => extra_args,
    'input_object_id' => input_object_id,
    'input_path' => input_path,
    'inputs' => inputs,
    'output_dir' => output_dir,
    'strategy' => strategy,
    'threads' => threads
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/msa/build',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeMsaBuildData.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

#msaCoevolution(alignment_object_id: nil, alignment_path: nil, max_gap_fraction: nil, max_sequences: nil, method_: nil, min_separation: nil, pseudocount: nil, reference: nil, reference_start: nil, reweight_identity: nil, top: nil, request_options: {}) ⇒ Rafflesia::EnvelopeCoevolutionData

POST /v1/sequences/msa/coevolution

Parameters:

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

    Object id containing aligned FASTA to analyse

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

    Aligned FASTA path to analyse

  • max_gap_fraction (Float, nil) (defaults to: nil) —

    Drop columns whose gap fraction exceeds this; 0 selects the default 0.5

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

    Cap on sequences used, evenly strided; 0 uses all

  • method (Rafflesia::Types::CoevolutionRequestMethod, nil) —

    Scoring method: dca (mean-field Direct Coupling Analysis, default) or mi (average-product-corrected mutual information, a weaker contact predictor shown for comparison)

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

    Minimum |i-j| in reference residue positions for a returned pair; 0 disables the separation filter

  • pseudocount (Float, nil) (defaults to: nil) —

    DCA pseudocount fraction; 0 selects the default 0.5

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

    Header first-token of the numbering reference sequence; defaults to the first record

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

    Residue number of the first ungapped reference position; 0 selects 1

  • reweight_identity (Float, nil) (defaults to: nil) —

    Sequence reweighting identity threshold in (0,1]; sequences sharing at least this fraction of columns share weight. 0 selects the default 0.8.

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

    Number of highest-scoring pairs to return; 0 returns all scored pairs

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 1860

def msaCoevolution(
  alignment_object_id: nil,
  alignment_path: nil,
  max_gap_fraction: nil,
  max_sequences: nil,
  method_: nil,
  min_separation: nil,
  pseudocount: nil,
  reference: nil,
  reference_start: nil,
  reweight_identity: nil,
  top: nil,
  request_options: {}
)
  body = {
    'alignment_object_id' => alignment_object_id,
    'alignment_path' => alignment_path,
    'max_gap_fraction' => max_gap_fraction,
    'max_sequences' => max_sequences,
    'method' => method_,
    'min_separation' => min_separation,
    'pseudocount' => pseudocount,
    'reference' => reference,
    'reference_start' => reference_start,
    'reweight_identity' => reweight_identity,
    'top' => top
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/msa/coevolution',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeCoevolutionData.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

#msaFromSearch(query:, cache_mode: nil, db: nil, dry_run: nil, extra_args: nil, hit_fasta_path: nil, homology_search_id: nil, include_query: nil, kmer_size: nil, max_hits: nil, min_identity: nil, output_dir: nil, search_backend: nil, search_object_id: nil, sequence_catalog_object_id: nil, strategy: nil, threads: nil, request_options: {}) ⇒ Rafflesia::EnvelopeMsaFromSearchData

POST /v1/sequences/msa/from-search

Parameters:

  • cache_mode (Rafflesia::Types::MsaFromSearchRequestCacheMode, nil) (defaults to: nil) —

    Artifact cache mode passed through to the MSA build

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

    FASTA database path searched before MSA construction; also used as the hit FASTA source when hit_fasta_path is omitted

  • dry_run (Boolean, nil) (defaults to: nil)
  • extra_args (Array<String>, nil) (defaults to: nil)
  • hit_fasta_path (String, nil) (defaults to: nil) —

    FASTA file containing target sequences named by the selected search hits

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

    Completed retained hsrch_ resource whose ordered target accessions seed the MSA

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

    Include the query sequence in the MSA input; defaults to true

  • kmer_size (Integer, nil) (defaults to: nil)
  • max_hits (Integer, nil) (defaults to: nil) —

    Maximum search hits to align; defaults to 20

  • min_identity (Float, nil) (defaults to: nil)
  • output_dir (String, nil) (defaults to: nil)
  • query (String) —

    Query sequence id or FASTA path

  • search_backend (Rafflesia::Types::MsaFromSearchRequestSearchBackend, nil) (defaults to: nil) —

    Search result backend to materialize; defaults to homology when homology_search_id is supplied, otherwise builtin unless search_object_id is supplied

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

    Object id containing a normalized search result envelope or data object

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

    Versioned sequence catalog object used to resolve search-hit ids into FASTA records

  • strategy (Rafflesia::Types::MsaFromSearchRequestStrategy, nil) (defaults to: nil)
  • threads (Integer, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 1919

def msaFromSearch(
  query:,
  cache_mode: nil,
  db: nil,
  dry_run: nil,
  extra_args: nil,
  hit_fasta_path: nil,
  homology_search_id: nil,
  include_query: nil,
  kmer_size: nil,
  max_hits: nil,
  min_identity: nil,
  output_dir: nil,
  search_backend: nil,
  search_object_id: nil,
  sequence_catalog_object_id: nil,
  strategy: nil,
  threads: nil,
  request_options: {}
)
  body = {
    'cache_mode' => cache_mode,
    'db' => db,
    'dry_run' => dry_run,
    'extra_args' => extra_args,
    'hit_fasta_path' => hit_fasta_path,
    'homology_search_id' => homology_search_id,
    'include_query' => include_query,
    'kmer_size' => kmer_size,
    'max_hits' => max_hits,
    'min_identity' => min_identity,
    'output_dir' => output_dir,
    'query' => query,
    'search_backend' => search_backend,
    'search_object_id' => search_object_id,
    'sequence_catalog_object_id' => sequence_catalog_object_id,
    'strategy' => strategy,
    'threads' => threads
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/msa/from-search',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeMsaFromSearchData.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

#msaInspect(alignment_object_id: nil, alignment_path: nil, database: nil, include_columns: nil, max_columns: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, relation: nil, release: nil, sort_by: nil, request_options: {}) ⇒ Rafflesia::EnvelopeMsaInspectData

POST /v1/sequences/msa/inspect

Parameters:

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

    Object id containing aligned FASTA to inspect

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

    Aligned FASTA path to inspect

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

    Database name published with the relation

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

    Include per-column conservation summaries

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

    Maximum number of column summaries to return when include_columns is true; 0 means all columns

  • output_format (Rafflesia::Types::MsaInspectRequestOutputFormat, 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/sequences.rb', line 1985

def msaInspect(
  alignment_object_id: nil,
  alignment_path: nil,
  database: nil,
  include_columns: nil,
  max_columns: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  request_options: {}
)
  body = {
    'alignment_object_id' => alignment_object_id,
    'alignment_path' => alignment_path,
    'database' => database,
    'include_columns' => include_columns,
    'max_columns' => max_columns,
    '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/sequences/msa/inspect',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeMsaInspectData.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

#profilesBuild(alignment_object_id: nil, alignment_path: nil, cache_mode: nil, dry_run: nil, extra_args: nil, name: nil, output_dir: nil, request_options: {}) ⇒ Rafflesia::EnvelopeProfileBuildData

POST /v1/sequences/profiles/build

Parameters:

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

    Object id containing aligned FASTA/MSA bytes

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

    Aligned FASTA/MSA path consumed by hmmbuild

  • cache_mode (Rafflesia::Types::ProfileBuildRequestCacheMode, nil) (defaults to: nil) —

    Artifact cache mode. use reuses matching cached profiles, refresh recomputes and stores, off recomputes without storing.

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

    Return the deterministic hmmbuild command without executing

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

    Explicit additional hmmbuild arguments

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

    Optional profile name passed to hmmbuild -n

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

    Directory for generated profile-HMM files

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 2036

def profilesBuild(
  alignment_object_id: nil,
  alignment_path: nil,
  cache_mode: nil,
  dry_run: nil,
  extra_args: nil,
  name: nil,
  output_dir: nil,
  request_options: {}
)
  body = {
    'alignment_object_id' => alignment_object_id,
    'alignment_path' => alignment_path,
    'cache_mode' => cache_mode,
    'dry_run' => dry_run,
    'extra_args' => extra_args,
    'name' => name,
    'output_dir' => output_dir
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/profiles/build',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeProfileBuildData.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(target_id:, allow_network: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSequenceData

POST /v1/sequences/records/fetch

Parameters:

  • allow_network (Boolean, nil) (defaults to: nil)
  • target_id (String)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 2072

def recordsFetch(
  target_id:,
  allow_network: nil,
  request_options: {}
)
  body = {
    'allow_network' => allow_network,
    'target_id' => target_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/records/fetch',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSequenceData.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:, target_id: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSequenceImportData

POST /v1/sequences/records/import

Parameters:

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 2098

def recordsImport(
  path:,
  target_id: nil,
  request_options: {}
)
  body = {
    'path' => path,
    'target_id' => target_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/records/import',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSequenceImportData.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

#recordsInspect(sequence_id:, request_options: {}) ⇒ Rafflesia::EnvelopeSequenceInspectData

POST /v1/sequences/records/inspect

Parameters:

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 2123

def recordsInspect(
  sequence_id:,
  request_options: {}
)
  body = {
    'sequence_id' => sequence_id
  }
  response = @client.request(
    method: :post,
    path: '/v1/sequences/records/inspect',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSequenceInspectData.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

#search(query:, database: nil, db: nil, kmer_size: nil, max_hits: nil, min_identity: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, relation: nil, release: nil, sort_by: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSequenceSearchData

POST /v1/sequences/search

Parameters:

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

    Database name published with the relation

  • db (String, nil) (defaults to: nil)
  • kmer_size (Integer, nil) (defaults to: nil)
  • max_hits (Integer, nil) (defaults to: nil)
  • min_identity (Float, nil) (defaults to: nil)
  • output_format (Rafflesia::Types::SequenceSearchRequestOutputFormat, 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

  • query (String)
  • 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/sequences.rb', line 2158

def search(
  query:,
  database: nil,
  db: nil,
  kmer_size: nil,
  max_hits: nil,
  min_identity: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  request_options: {}
)
  body = {
    'database' => database,
    'db' => db,
    'kmer_size' => kmer_size,
    'max_hits' => max_hits,
    'min_identity' => min_identity,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'query' => query,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/search',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSequenceSearchData.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

#searchBlast(query:, concurrency: nil, database: nil, db: nil, db_refs: nil, dry_run: nil, evalue: nil, manifest_path: nil, materialize: nil, max_exact_shards: nil, max_materialized_bytes: nil, max_object_bytes: nil, max_object_reads: nil, max_target_seqs: nil, min_bit_score: nil, out_format: nil, output_dir: nil, output_format: nil, output_relation: nil, pack_access_mode: nil, partition_by: nil, preview_limit: nil, profile: nil, program: nil, relation: nil, release: nil, require_routing: nil, require_zero_materialization: nil, routing_concurrency: nil, routing_index_id: nil, routing_kmer_size: nil, routing_manifest_object_id: nil, routing_manifest_path: nil, routing_max_candidates: nil, routing_min_identity: nil, routing_name: nil, routing_rerank_alignment: nil, routing_use_block_cache: nil, routing_version: nil, routing_wal_object_ids: nil, shard_ids: nil, sort_by: nil, target_dir: nil, task: nil, threads: nil, request_options: {}) ⇒ Rafflesia::EnvelopeBlastSearchData

POST /v1/sequences/search/blast

Parameters:

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

    Maximum BLAST shard searches to execute concurrently when db_refs is set; defaults to 4.

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

    Database name published with the relation

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

    Published BLAST DB ref, manifest path, or materialized DB prefix

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

    Optional published BLAST DB refs to search as independent shards; when set, db is optional.

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

    Return the deterministic command without executing BLAST

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

    BLAST e-value threshold; passed through as text

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

    Optional manifest path when db is not a published ref

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

    Whether to materialize DB artifacts before search; defaults to true for manifests/refs

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

    Optional hard cap on exact BLAST shards searched after routing or explicit selection.

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

    Optional hard cap on planned local bytes materialized before exact BLAST scoring.

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

    Optional hard cap on planned object-store bytes read for routing or materialization.

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

    Optional hard cap on planned object-store reads for routing or materialization.

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

    Maximum target sequences; defaults to 100

  • min_bit_score (Float, nil) (defaults to: nil) —

    Optional client-visible hit filter applied after BLAST tabular parsing

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

    BLAST outfmt value; defaults to deterministic tabular fields

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

    Directory for raw BLAST result artifacts

  • output_format (Rafflesia::Types::BlastSearchRequestOutputFormat, 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

  • pack_access_mode (Rafflesia::Types::BlastSearchRequestPackAccessMode, nil) (defaults to: nil) —

    For rafflesia_pack indexes, choose local materialization or direct object-store range reads; auto prefers remote_range when executable object URLs are available. object_native requires a routing seed index and scores selected payload records in-process without a BLAST DB.

  • 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

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

    Include per-phase wall-clock timing (query resolve, DB materialize, BLAST search, normalized-output store) in the response.

  • program (Rafflesia::Types::BlastSearchRequestProgram, nil) (defaults to: nil) —

    BLAST executable; defaults to blastp

  • query (String) —

    Query FASTA path or cached sequence id

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

    Requested logical relation name

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

    Immutable database release published with the relation

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

    Require a routing index or candidate-pruned path instead of a full exact search over every selected shard.

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

    Require the planned path to materialize zero local database bytes before exact BLAST scoring.

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

    Maximum concurrent object reads for the routing seed index; defaults to 8.

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

    Published sequence seed-index id used to preselect BLAST candidate subjects.

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

    Optional query k-mer size for the routing seed index; must match the index k-mer size when set.

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

    Object id for an object-backed sequence seed index used to preselect BLAST candidate subjects before exact BLAST scoring.

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

    Local sequence seed-index manifest used to preselect BLAST candidate subjects before exact BLAST scoring.

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

    Maximum seed-index candidates selected for exact BLAST scoring; defaults to max_target_seqs.

  • routing_min_identity (Float, nil) (defaults to: nil) —

    Minimum seed-index k-mer identity fraction for BLAST candidate preselection.

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

    Published sequence seed-index name used with routing_version to preselect BLAST candidate subjects.

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

    When true, Needleman-Wunsch reranks seed-index candidates before exact BLAST scoring.

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

    Whether to use the process-local seed-index object block cache during routing; defaults to true.

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

    Published sequence seed-index version used with routing_name to preselect BLAST candidate subjects.

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

    Optional sequence seed-index WAL objects to overlay during BLAST candidate routing.

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

    Optional shard ids corresponding to db_refs; defaults to the db ref value.

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

    Requested physical sort columns

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

    Local cache directory for materialized DB files

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

    Optional BLAST task

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

    Number of BLAST threads; defaults to 1

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 2249

def searchBlast(
  query:,
  concurrency: nil,
  database: nil,
  db: nil,
  db_refs: nil,
  dry_run: nil,
  evalue: nil,
  manifest_path: nil,
  materialize: nil,
  max_exact_shards: nil,
  max_materialized_bytes: nil,
  max_object_bytes: nil,
  max_object_reads: nil,
  max_target_seqs: nil,
  min_bit_score: nil,
  out_format: nil,
  output_dir: nil,
  output_format: nil,
  output_relation: nil,
  pack_access_mode: nil,
  partition_by: nil,
  preview_limit: nil,
  profile: nil,
  program: nil,
  relation: nil,
  release: nil,
  require_routing: nil,
  require_zero_materialization: nil,
  routing_concurrency: nil,
  routing_index_id: nil,
  routing_kmer_size: nil,
  routing_manifest_object_id: nil,
  routing_manifest_path: nil,
  routing_max_candidates: nil,
  routing_min_identity: nil,
  routing_name: nil,
  routing_rerank_alignment: nil,
  routing_use_block_cache: nil,
  routing_version: nil,
  routing_wal_object_ids: nil,
  shard_ids: nil,
  sort_by: nil,
  target_dir: nil,
  task: nil,
  threads: nil,
  request_options: {}
)
  body = {
    'concurrency' => concurrency,
    'database' => database,
    'db' => db,
    'db_refs' => db_refs,
    'dry_run' => dry_run,
    'evalue' => evalue,
    'manifest_path' => manifest_path,
    'materialize' => materialize,
    'max_exact_shards' => max_exact_shards,
    'max_materialized_bytes' => max_materialized_bytes,
    'max_object_bytes' => max_object_bytes,
    'max_object_reads' => max_object_reads,
    'max_target_seqs' => max_target_seqs,
    'min_bit_score' => min_bit_score,
    'out_format' => out_format,
    'output_dir' => output_dir,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'pack_access_mode' => pack_access_mode,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'profile' => profile,
    'program' => program,
    'query' => query,
    'relation' => relation,
    'release' => release,
    'require_routing' => require_routing,
    'require_zero_materialization' => require_zero_materialization,
    'routing_concurrency' => routing_concurrency,
    'routing_index_id' => routing_index_id,
    'routing_kmer_size' => routing_kmer_size,
    'routing_manifest_object_id' => routing_manifest_object_id,
    'routing_manifest_path' => routing_manifest_path,
    'routing_max_candidates' => routing_max_candidates,
    'routing_min_identity' => routing_min_identity,
    'routing_name' => routing_name,
    'routing_rerank_alignment' => routing_rerank_alignment,
    'routing_use_block_cache' => routing_use_block_cache,
    'routing_version' => routing_version,
    'routing_wal_object_ids' => routing_wal_object_ids,
    'shard_ids' => shard_ids,
    'sort_by' => sort_by,
    'target_dir' => target_dir,
    'task' => task,
    'threads' => threads
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/search/blast',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeBlastSearchData.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

#searchBlastBenchmark(query:, db: nil, evalue: nil, manifest_path: nil, max_local_control_bytes: nil, max_object_bytes: nil, max_object_reads: nil, max_target_seqs: nil, min_bit_score: nil, min_byte_reduction_fraction: nil, min_hit_overlap_fraction: nil, min_recall_at_1: nil, min_recall_at_10: nil, output_dir: nil, profile: nil, program: nil, require_exact_pack_reads: nil, require_no_local_control_files: nil, require_zero_materialization: nil, routing_concurrency: nil, routing_index_id: nil, routing_kmer_size: nil, routing_manifest_object_id: nil, routing_manifest_path: nil, routing_max_candidates: nil, routing_min_identity: nil, routing_name: nil, routing_rerank_alignment: nil, routing_use_block_cache: nil, routing_version: nil, store_artifact: nil, target_dir: nil, request_options: {}) ⇒ Rafflesia::EnvelopeBlastSearchBenchmarkData

POST /v1/sequences/search/blast/benchmark

Parameters:

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

    Published BLAST DB ref, manifest path, or materialized DB prefix used by the materialized baseline search.

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

    BLAST e-value threshold passed to the baseline search and recorded on object-native search.

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

    Optional BLAST DB manifest path used by the materialized baseline search.

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

    Optional hard pass threshold for object-native local control bytes.

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

    Optional hard pass threshold for object-native object bytes fetched.

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

    Optional hard pass threshold for object-native object reads.

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

    Maximum hits returned by each search; defaults to 100.

  • min_bit_score (Float, nil) (defaults to: nil) —

    Optional visible hit filter applied to both search responses.

  • min_byte_reduction_fraction (Float, nil) (defaults to: nil) —

    Optional pass threshold for object-native byte reduction versus materialized baseline bytes.

  • min_hit_overlap_fraction (Float, nil) (defaults to: nil) —

    Optional pass threshold for full returned-hit overlap against the materialized baseline.

  • min_recall_at_1 (Float, nil) (defaults to: nil) —

    Optional pass threshold for recall@1 against the materialized baseline.

  • min_recall_at_10 (Float, nil) (defaults to: nil) —

    Optional pass threshold for recall@10 against the materialized baseline.

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

    Directory for raw baseline BLAST result artifacts.

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

    Include per-search wall-clock profiles in the nested search responses.

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

    BLAST executable family to benchmark; currently blastp.

  • query (String) —

    Query FASTA path or cached sequence id used for both baseline and object-native searches.

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

    Require object-native exact scoring to read selected Rafflesia pack blocks from object storage.

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

    Require object-native exact scoring to avoid writing local candidate/control files.

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

    Require object-native search to materialize zero database bytes.

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

    Maximum concurrent object reads for object-native routing.

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

    Published sequence seed-index id used by object-native search.

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

    Optional query k-mer size for object-native routing.

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

    Object id for the sequence seed index used by object-native search.

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

    Local sequence seed-index manifest used by object-native search.

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

    Maximum seed-index candidates selected for object-native scoring; defaults to max_target_seqs.

  • routing_min_identity (Float, nil) (defaults to: nil) —

    Minimum seed-index k-mer identity fraction for object-native candidate preselection.

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

    Published sequence seed-index name used with routing_version.

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

    When true, Needleman-Wunsch reranks seed-index candidates before object-native scoring.

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

    Whether to use the process-local seed-index object block cache during object-native routing.

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

    Published sequence seed-index version used with routing_name.

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

    Store the benchmark JSON artifact in object storage; defaults to true.

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

    Local cache directory for the materialized baseline search.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 2459

def searchBlastBenchmark(
  query:,
  db: nil,
  evalue: nil,
  manifest_path: nil,
  max_local_control_bytes: nil,
  max_object_bytes: nil,
  max_object_reads: nil,
  max_target_seqs: nil,
  min_bit_score: nil,
  min_byte_reduction_fraction: nil,
  min_hit_overlap_fraction: nil,
  min_recall_at_1: nil,
  min_recall_at_10: nil,
  output_dir: nil,
  profile: nil,
  program: nil,
  require_exact_pack_reads: nil,
  require_no_local_control_files: nil,
  require_zero_materialization: nil,
  routing_concurrency: nil,
  routing_index_id: nil,
  routing_kmer_size: nil,
  routing_manifest_object_id: nil,
  routing_manifest_path: nil,
  routing_max_candidates: nil,
  routing_min_identity: nil,
  routing_name: nil,
  routing_rerank_alignment: nil,
  routing_use_block_cache: nil,
  routing_version: nil,
  store_artifact: nil,
  target_dir: nil,
  request_options: {}
)
  body = {
    'db' => db,
    'evalue' => evalue,
    'manifest_path' => manifest_path,
    'max_local_control_bytes' => max_local_control_bytes,
    'max_object_bytes' => max_object_bytes,
    'max_object_reads' => max_object_reads,
    'max_target_seqs' => max_target_seqs,
    'min_bit_score' => min_bit_score,
    'min_byte_reduction_fraction' => min_byte_reduction_fraction,
    'min_hit_overlap_fraction' => min_hit_overlap_fraction,
    'min_recall_at_1' => min_recall_at_1,
    'min_recall_at_10' => min_recall_at_10,
    'output_dir' => output_dir,
    'profile' => profile,
    'program' => program,
    'query' => query,
    'require_exact_pack_reads' => require_exact_pack_reads,
    'require_no_local_control_files' => require_no_local_control_files,
    'require_zero_materialization' => require_zero_materialization,
    'routing_concurrency' => routing_concurrency,
    'routing_index_id' => routing_index_id,
    'routing_kmer_size' => routing_kmer_size,
    'routing_manifest_object_id' => routing_manifest_object_id,
    'routing_manifest_path' => routing_manifest_path,
    'routing_max_candidates' => routing_max_candidates,
    'routing_min_identity' => routing_min_identity,
    'routing_name' => routing_name,
    'routing_rerank_alignment' => routing_rerank_alignment,
    'routing_use_block_cache' => routing_use_block_cache,
    'routing_version' => routing_version,
    'store_artifact' => store_artifact,
    'target_dir' => target_dir
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/search/blast/benchmark',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeBlastSearchBenchmarkData.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

#searchBlastCatalog(catalog:, query:, store_root:, concurrency: nil, database: nil, evalue: nil, max_target_seqs: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, program: nil, relation: nil, release: nil, sort_by: nil, threads: nil, request_options: {}) ⇒ Rafflesia::EnvelopeBlastSearchData

POST /v1/sequences/search/blast-catalog

Parameters:

  • catalog (String) —

    Object key of the catalog JSON within the store

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

    Max shard searches in parallel; defaults to the coordinator default

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

    Database name published with the relation

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

    BLAST e-value threshold; passed through as text

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

    Maximum target sequences; defaults to 100

  • output_format (Rafflesia::Types::BlastCatalogSearchRequestOutputFormat, 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

  • program (Rafflesia::Types::BlastCatalogSearchRequestProgram, nil) (defaults to: nil) —

    BLAST executable; defaults to blastp

  • query (String) —

    Query FASTA path or cached sequence id

  • 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

  • store_root (String) —

    Object-store root: a path/file:// for a local bucket, or s3://bucket/prefix

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

    BLAST threads per shard; defaults to 1

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 2375

def searchBlastCatalog(
  catalog:,
  query:,
  store_root:,
  concurrency: nil,
  database: nil,
  evalue: nil,
  max_target_seqs: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  program: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  threads: nil,
  request_options: {}
)
  body = {
    'catalog' => catalog,
    'concurrency' => concurrency,
    'database' => database,
    'evalue' => evalue,
    'max_target_seqs' => max_target_seqs,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'program' => program,
    'query' => query,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by,
    'store_root' => store_root,
    'threads' => threads
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/search/blast-catalog',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeBlastSearchData.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

#searchBlastExplain(search:, workload_profile: nil, request_options: {}) ⇒ Rafflesia::EnvelopeBlastSearchExplainData

POST /v1/sequences/search/blast/explain

Parameters:

  • search (Rafflesia::BlastSearchRequest)
  • workload_profile (String, nil) (defaults to: nil) —

    Optional workload profile name such as blast-small or blast-large.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 2545

def searchBlastExplain(
  search:,
  workload_profile: nil,
  request_options: {}
)
  body = {
    'search' => search,
    'workload_profile' => workload_profile
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/search/blast/explain',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeBlastSearchExplainData.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

#searchCandidates(namespace:, query:, max_hits: nil, max_object_bytes: nil, max_object_reads: nil, query_mode: nil, require_zero_materialization: nil, timeout_ms: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSequenceCandidateSearchData

POST /v1/sequences/search/candidates

Parameters:

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

    Maximum number of hits returned; defaults to 10.

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

    Optional hard budget checked against observed object bytes.

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

    Optional hard budget checked against observed object reads.

  • namespace (String) —

    Sequence candidate namespace to search.

  • query (String) —

    Query sequence ID, literal sequence, or local FASTA path.

  • query_mode (Rafflesia::Types::SequenceCandidateSearchRequestQueryMode, nil) (defaults to: nil) —

    Candidate serving mode. bounded_fast avoids full payload fallback; exact_safe may scan payload shards to certify top-k.

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

    Require the object-native path to materialize zero local database bytes.

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

    Hard deadline for this search in milliseconds; defaults to the sequence candidate search timeout.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 2577

def searchCandidates(
  namespace:,
  query:,
  max_hits: nil,
  max_object_bytes: nil,
  max_object_reads: nil,
  query_mode: nil,
  require_zero_materialization: nil,
  timeout_ms: nil,
  request_options: {}
)
  body = {
    'max_hits' => max_hits,
    'max_object_bytes' => max_object_bytes,
    'max_object_reads' => max_object_reads,
    'namespace' => namespace,
    'query' => query,
    'query_mode' => query_mode,
    'require_zero_materialization' => require_zero_materialization,
    'timeout_ms' => timeout_ms
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/search/candidates',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSequenceCandidateSearchData.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

#searchDiamond(query:, database: nil, db: nil, dry_run: nil, evalue: nil, extra_args: nil, manifest_path: nil, materialize: nil, max_target_seqs: nil, min_bit_score: nil, out_format: nil, output_dir: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, program: nil, query_gencode: nil, relation: nil, release: nil, sort_by: nil, target_dir: nil, threads: nil, request_options: {}) ⇒ Rafflesia::EnvelopeDiamondSearchData

POST /v1/sequences/search/diamond

Parameters:

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

    Database name published with the relation

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

    Published DIAMOND DB ref, manifest path, or materialized database prefix/path

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

    Return the deterministic command without executing DIAMOND

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

    DIAMOND E-value threshold; passed through as text

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

    Explicit additional DIAMOND search arguments

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

    Optional manifest path when db is not a published ref

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

    Whether to materialize DB artifacts before search; defaults to true for manifests/refs

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

    Maximum target sequences; defaults to 100

  • min_bit_score (Float, nil) (defaults to: nil) —

    Optional client-visible hit filter applied after parsing

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

    DIAMOND outfmt value; defaults to deterministic tabular fields

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

    Directory for raw DIAMOND result artifacts

  • output_format (Rafflesia::Types::DiamondSearchRequestOutputFormat, 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

  • program (Rafflesia::Types::DiamondSearchRequestProgram, nil) (defaults to: nil) —

    DIAMOND executable mode; defaults to blastp

  • query (String) —

    Query FASTA path or cached sequence id

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

    Optional query genetic code for translated search

  • 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

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

    Local cache directory for materialized DIAMOND DB files

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

    Number of DIAMOND threads; defaults to 1

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 2636

def searchDiamond(
  query:,
  database: nil,
  db: nil,
  dry_run: nil,
  evalue: nil,
  extra_args: nil,
  manifest_path: nil,
  materialize: nil,
  max_target_seqs: nil,
  min_bit_score: nil,
  out_format: nil,
  output_dir: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  program: nil,
  query_gencode: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  target_dir: nil,
  threads: nil,
  request_options: {}
)
  body = {
    'database' => database,
    'db' => db,
    'dry_run' => dry_run,
    'evalue' => evalue,
    'extra_args' => extra_args,
    'manifest_path' => manifest_path,
    'materialize' => materialize,
    'max_target_seqs' => max_target_seqs,
    'min_bit_score' => min_bit_score,
    'out_format' => out_format,
    'output_dir' => output_dir,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'program' => program,
    'query' => query,
    'query_gencode' => query_gencode,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by,
    'target_dir' => target_dir,
    'threads' => threads
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/search/diamond',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeDiamondSearchData.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

#searchDiamondCatalog(catalog:, query:, store_root:, concurrency: nil, database: nil, evalue: nil, max_target_seqs: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, program: nil, relation: nil, release: nil, sort_by: nil, threads: nil, request_options: {}) ⇒ Rafflesia::EnvelopeDiamondSearchData

POST /v1/sequences/search/diamond-catalog

Parameters:

  • catalog (String) —

    Object key of the catalog JSON within the store

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

    Max shard searches in parallel; defaults to the coordinator default

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

    Database name published with the relation

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

    DIAMOND e-value threshold; passed through as text

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

    Maximum target sequences; defaults to 100

  • output_format (Rafflesia::Types::DiamondCatalogSearchRequestOutputFormat, 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

  • program (Rafflesia::Types::DiamondCatalogSearchRequestProgram, nil) (defaults to: nil) —

    DIAMOND mode; defaults to blastp

  • query (String) —

    Query FASTA path or cached sequence id

  • 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

  • store_root (String) —

    Object-store root: a path/file:// for a local bucket, or s3://bucket/prefix

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

    DIAMOND threads per shard; defaults to 1

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 2718

def searchDiamondCatalog(
  catalog:,
  query:,
  store_root:,
  concurrency: nil,
  database: nil,
  evalue: nil,
  max_target_seqs: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  program: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  threads: nil,
  request_options: {}
)
  body = {
    'catalog' => catalog,
    'concurrency' => concurrency,
    'database' => database,
    'evalue' => evalue,
    'max_target_seqs' => max_target_seqs,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'program' => program,
    'query' => query,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by,
    'store_root' => store_root,
    'threads' => threads
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/search/diamond-catalog',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeDiamondSearchData.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

#searchHmmer(database: nil, db: nil, domains: nil, dry_run: nil, evalue: nil, extra_args: nil, manifest_object_id: nil, manifest_path: nil, output_dir: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, program: nil, query: nil, relation: nil, release: nil, shards: nil, sort_by: nil, target_dir: nil, threads: nil, request_options: {}) ⇒ Rafflesia::EnvelopeHmmerSearchData

POST /v1/sequences/search/hmmer

Parameters:

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

    Database name published with the relation

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

    Target database path; optional when manifest contains an hmmer_db artifact

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

    Use --domtblout and return per-domain hits

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

    Return the deterministic command without executing HMMER

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

    HMMER E-value threshold; passed through as text

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

    Explicit additional HMMER arguments

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

    Optional neutral object-artifact manifest object id

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

    Optional neutral object-artifact manifest path containing hmmer_db and optional query artifacts

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

    Directory for raw HMMER result artifacts

  • output_format (Rafflesia::Types::HmmerSearchRequestOutputFormat, 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

  • program (Rafflesia::Types::HmmerSearchRequestProgram, nil) (defaults to: nil) —

    HMMER executable; defaults to hmmsearch

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

    Query profile/sequence path or cached sequence id; optional when manifest contains a query artifact

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

    Requested logical relation name

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

    Immutable database release published with the relation

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

    Optional shard ids to materialize from the manifest

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

    Requested physical sort columns

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

    Local cache root for materialized HMMER artifacts

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

    Number of HMMER CPU threads; defaults to 1

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 2791

def searchHmmer(
  database: nil,
  db: nil,
  domains: nil,
  dry_run: nil,
  evalue: nil,
  extra_args: nil,
  manifest_object_id: nil,
  manifest_path: nil,
  output_dir: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  program: nil,
  query: nil,
  relation: nil,
  release: nil,
  shards: nil,
  sort_by: nil,
  target_dir: nil,
  threads: nil,
  request_options: {}
)
  body = {
    'database' => database,
    'db' => db,
    'domains' => domains,
    'dry_run' => dry_run,
    'evalue' => evalue,
    'extra_args' => extra_args,
    'manifest_object_id' => manifest_object_id,
    'manifest_path' => manifest_path,
    'output_dir' => output_dir,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'program' => program,
    'query' => query,
    'relation' => relation,
    'release' => release,
    'shards' => shards,
    'sort_by' => sort_by,
    'target_dir' => target_dir,
    'threads' => threads
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/search/hmmer',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeHmmerSearchData.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

#searchHmmerCatalog(catalog:, query:, store_root:, concurrency: nil, database: nil, evalue: nil, limit: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, program: nil, relation: nil, release: nil, sort_by: nil, threads: nil, request_options: {}) ⇒ Rafflesia::EnvelopeHmmerSearchData

POST /v1/sequences/search/hmmer-catalog

Parameters:

  • catalog (String) —

    Object key of the catalog JSON within the store

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

    Max shard searches in parallel; defaults to the coordinator default

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

    Database name published with the relation

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

    HMMER E-value threshold; passed through as text

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

    Maximum merged hits; defaults to 50

  • output_format (Rafflesia::Types::HmmerCatalogSearchRequestOutputFormat, 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

  • program (Rafflesia::Types::HmmerCatalogSearchRequestProgram, nil) (defaults to: nil) —

    HMMER executable; defaults to hmmsearch

  • query (String) —

    Query profile/sequence path or cached sequence id

  • 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

  • store_root (String) —

    Object-store root: a path/file:// for a local bucket, or s3://bucket/prefix

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

    HMMER threads per shard; defaults to 1

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 2869

def searchHmmerCatalog(
  catalog:,
  query:,
  store_root:,
  concurrency: nil,
  database: nil,
  evalue: nil,
  limit: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  program: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  threads: nil,
  request_options: {}
)
  body = {
    'catalog' => catalog,
    'concurrency' => concurrency,
    'database' => database,
    'evalue' => evalue,
    'limit' => limit,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'program' => program,
    'query' => query,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by,
    'store_root' => store_root,
    'threads' => threads
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/search/hmmer-catalog',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeHmmerSearchData.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

#searchMmseqs(query:, database: nil, dry_run: nil, extra_args: nil, manifest_object_id: nil, manifest_path: nil, max_seqs: nil, min_bits: nil, output_dir: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, relation: nil, release: nil, sensitivity: nil, shards: nil, sort_by: nil, target: nil, target_dir: nil, threads: nil, request_options: {}) ⇒ Rafflesia::EnvelopeMmseqsSearchData

POST /v1/sequences/search/mmseqs

Parameters:

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

    Database name published with the relation

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

    Return the deterministic command without executing MMseqs2

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

    Explicit additional MMseqs2 arguments

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

    Optional neutral object-artifact manifest object id

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

    Optional neutral object-artifact manifest path containing mmseqs_db_base artifacts

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

    Maximum sequences per query; defaults to 300

  • min_bits (Float, nil) (defaults to: nil) —

    Optional client-visible hit filter applied after parsing

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

    Directory for raw MMseqs2 result artifacts

  • output_format (Rafflesia::Types::MmseqSearchRequestOutputFormat, 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

  • query (String) —

    Query FASTA path or cached sequence id

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

    Requested logical relation name

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

    Immutable database release published with the relation

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

    Optional MMseqs2 -s sensitivity value

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

    Optional shard ids to materialize from the manifest

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

    Requested physical sort columns

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

    MMseqs2 target database or FASTA path; optional when manifest contains a mmseqs_db_base artifact

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

    Local cache root for materialized MMseqs2 artifacts

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

    Number of MMseqs2 threads; defaults to 1

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 2942

def searchMmseqs(
  query:,
  database: nil,
  dry_run: nil,
  extra_args: nil,
  manifest_object_id: nil,
  manifest_path: nil,
  max_seqs: nil,
  min_bits: nil,
  output_dir: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  relation: nil,
  release: nil,
  sensitivity: nil,
  shards: nil,
  sort_by: nil,
  target: nil,
  target_dir: nil,
  threads: nil,
  request_options: {}
)
  body = {
    'database' => database,
    'dry_run' => dry_run,
    'extra_args' => extra_args,
    'manifest_object_id' => manifest_object_id,
    'manifest_path' => manifest_path,
    'max_seqs' => max_seqs,
    'min_bits' => min_bits,
    'output_dir' => output_dir,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'query' => query,
    'relation' => relation,
    'release' => release,
    'sensitivity' => sensitivity,
    'shards' => shards,
    'sort_by' => sort_by,
    'target' => target,
    'target_dir' => target_dir,
    'threads' => threads
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/search/mmseqs',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeMmseqsSearchData.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

#searchMmseqsCatalog(catalog:, query:, store_root:, concurrency: nil, database: nil, max_seqs: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, relation: nil, release: nil, sensitivity: nil, sort_by: nil, threads: nil, request_options: {}) ⇒ Rafflesia::EnvelopeMmseqsSearchData

POST /v1/sequences/search/mmseqs-catalog

Parameters:

  • catalog (String) —

    Object key of the catalog JSON within the store

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

    Max shard searches in parallel; defaults to the coordinator default

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

    Database name published with the relation

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

    Maximum sequences per query; defaults to 300

  • output_format (Rafflesia::Types::MmseqCatalogSearchRequestOutputFormat, 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

  • query (String) —

    Query FASTA path or cached sequence id

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

    Requested logical relation name

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

    Immutable database release published with the relation

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

    Optional MMseqs2 -s sensitivity value

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

    Requested physical sort columns

  • store_root (String) —

    Object-store root: a path/file:// for a local bucket, or s3://bucket/prefix

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

    MMseqs2 threads per shard; defaults to 1

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 3019

def searchMmseqsCatalog(
  catalog:,
  query:,
  store_root:,
  concurrency: nil,
  database: nil,
  max_seqs: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  relation: nil,
  release: nil,
  sensitivity: nil,
  sort_by: nil,
  threads: nil,
  request_options: {}
)
  body = {
    'catalog' => catalog,
    'concurrency' => concurrency,
    'database' => database,
    'max_seqs' => max_seqs,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'query' => query,
    'relation' => relation,
    'release' => release,
    'sensitivity' => sensitivity,
    'sort_by' => sort_by,
    'store_root' => store_root,
    'threads' => threads
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/search/mmseqs-catalog',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeMmseqsSearchData.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

#searchSeedIndex(query:, concurrency: nil, database: nil, index_id: nil, kmer_size: nil, manifest_object_id: nil, manifest_path: nil, max_hits: nil, max_object_bytes: nil, max_object_reads: nil, min_identity: nil, name: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, relation: nil, release: nil, require_zero_materialization: nil, rerank_alignment: nil, sort_by: nil, use_block_cache: nil, version: nil, wal_object_ids: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSequenceSearchData

POST /v1/sequences/search/seed-index

Parameters:

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

    Maximum concurrent object block reads; defaults to 8

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

    Database name published with the relation

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

    Published sequence seed index id

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

    Optional query k-mer size; must match the index k-mer size when set

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

    Object id for a sequence seed index manifest

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

    Local path to a sequence seed index manifest JSON file

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

    Maximum number of candidate subjects returned; defaults to 100

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

    Optional hard execution budget for object bytes. Search fails before fetching blocks when the budget would be exceeded.

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

    Optional hard execution budget for object reads. Search fails before fetching blocks when the budget would be exceeded.

  • min_identity (Float, nil) (defaults to: nil) —

    Minimum fraction of distinct query k-mers present in a subject

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

    Published sequence seed index name

  • output_format (Rafflesia::Types::SequenceSeedIndexSearchRequestOutputFormat, 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

  • query (String) —

    Sequence ID or local FASTA path for query sequence

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

    Requested logical relation name

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

    Immutable database release published with the relation

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

    Require the object-native execution path to materialize zero database bytes

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

    When true, run deterministic Needleman-Wunsch alignment over returned candidates and sort by alignment identity

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

    Requested physical sort columns

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

    Whether to use the process-local seed-index object block cache; defaults to true in the server

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

    Published sequence seed index version

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

    Optional sequence seed-index WAL objects to overlay on the immutable index before compaction

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/sequences.rb', line 3093

def searchSeedIndex(
  query:,
  concurrency: nil,
  database: nil,
  index_id: nil,
  kmer_size: nil,
  manifest_object_id: nil,
  manifest_path: nil,
  max_hits: nil,
  max_object_bytes: nil,
  max_object_reads: nil,
  min_identity: nil,
  name: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  relation: nil,
  release: nil,
  require_zero_materialization: nil,
  rerank_alignment: nil,
  sort_by: nil,
  use_block_cache: nil,
  version: nil,
  wal_object_ids: nil,
  request_options: {}
)
  body = {
    'concurrency' => concurrency,
    'database' => database,
    'index_id' => index_id,
    'kmer_size' => kmer_size,
    'manifest_object_id' => manifest_object_id,
    'manifest_path' => manifest_path,
    'max_hits' => max_hits,
    'max_object_bytes' => max_object_bytes,
    'max_object_reads' => max_object_reads,
    'min_identity' => min_identity,
    'name' => name,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'query' => query,
    'relation' => relation,
    'release' => release,
    'require_zero_materialization' => require_zero_materialization,
    'rerank_alignment' => rerank_alignment,
    'sort_by' => sort_by,
    'use_block_cache' => use_block_cache,
    'version' => version,
    'wal_object_ids' => wal_object_ids
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/sequences/search/seed-index',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSequenceSearchData.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