@rcsb/rcsb-saguaro-app 6.3.2-dev-js-seqcoord.13 → 6.3.3

package/lib/RcsbQueries/Borrego/schema.graphql

@@ -1,47 +1,31 @@
-# This file was generated. Do not edit manually.
+# This file was generated based on ".graphqlconfig". Do not edit manually.
 
 schema {
     query: Query
-    subscription: Subscription
 }
 
-"Indicates an Input Object is a OneOf Input Object."
-directive @oneOf on INPUT_OBJECT
-
-type AlignedRegions {
-    "List of genomic indexes that are needed to complete the last nucleotide codon of a genome-protein sequence alignment"
-    exon_shift: [Int]
+type AdditionalProperty {
     """
 
-    Query sequence start position
+    The additional property name.
 
     Examples:
-    null, null
-    """
-    query_begin: Int!
+    PARENT_COMP_ID, CATH_NAME, PARTNER_BOND_DISTANCE
     """
+    property_name: PropertyName
+    property_value: [ObjectScalar]
+}
 
-    Query sequence end position
-
-    Examples:
-    null, null
-    """
+type AlignedRegion {
+    "List of genomic indexes that are needed to complete the last nucleotide triad of a genome-protein sequence alignment"
+    exon_shift: [Int]
+    "Query sequence start position"
+    query_begin: Int!
+    "Query sequence end position"
     query_end: Int!
-    """
-
-    Target sequence start position
-
-    Examples:
-    null, null
-    """
+    "Target sequence start position"
     target_begin: Int!
-    """
-
-    Target sequence start position
-
-    Examples:
-    null, null
-    """
+    "Target sequence start position"
     target_end: Int!
 }
 
@@ -50,77 +34,50 @@ type AlignmentLogo {
     value: Int
 }
 
-type Coverage {
-    """
-
-    Fraction of the query sequence covered by the alignment
-
-    Examples:
-    null, null
-    """
-    query_coverage: Float!
-    """
-
-    Length of the full query sequence
-
-    Examples:
-    null, null
-    """
-    query_length: Int!
-    """
-
-    Fraction of the target sequence covered by the alignment
-
-    Examples:
-    null, null
-    """
-    target_coverage: Float!
-    """
-
-    Length of the full target sequence
-
-    Examples:
-    null, null
-    """
-    target_length: Int!
+type AlignmentResponse {
+    "Length of the alignment"
+    alignment_length: Int
+    alignment_logo: [[AlignmentLogo]]
+    "Full sequence of the query"
+    query_sequence: String
+    "JSON schema that describes the different alignments between the query sequence and targets"
+    target_alignment: [TargetAlignment]
+    "Multiple sequence alignment of group members."
+    target_alignment_subset(after: String, first: Int!): TargetAlignmentConnection
 }
 
-type Features {
-    "Attribute/Value list"
-    additional_properties: [FeaturesAdditionalProperties]
-    """
+type AnnotationFeatures {
+    "List of positional features"
+    features: [Feature]
+    "Enumerated value that identifies the provenance type of the positional features"
+    source: Source
+    "Database source entry identifier associated to the positional features"
+    target_id: String
+    target_identifiers: TargetIdentifiers
+}
 
-    Free-form text describing the feature
+type Coverage {
+    "Percentage of the query sequence covered byt the alignment"
+    query_coverage: Int
+    "Length of the full query sequence"
+    query_length: Int
+    "Percentage of the target sequence covered byt the alignment"
+    target_coverage: Int
+    "Length of the full target sequence"
+    target_length: Int
+}
 
-    Examples:
-    Software generated binding site for ligand entity 2 component HEM instance C chain A
-    """
+type Feature {
+    additional_properties: [AdditionalProperty]
+    "Free-form text describing the feature"
     description: String
-    """
-
-    Identifier of the feature
-
-    Examples:
-    HELX_P11, AC1
-    """
+    "Identifier of the feature"
     feature_id: String
-    "List of documents that describes the location of the feature"
-    feature_positions: [FeaturesFeaturePositions]
-    """
-
-    Name associated to the feature
-
-    Examples:
-    ligand HEM
-    """
+    " List of documents that describes the location of the feature"
+    feature_positions: [FeaturePosition]
+    "Name associated to the feature"
     name: String
-    """
-
-    Original database or software name used to obtain the feature
-
-    Examples:
-    PDB, UNIPROT
-    """
+    "Original database or software name used to obtain the feature"
     provenance_source: String
     """
 
@@ -129,311 +86,140 @@ type Features {
     Examples:
     ASA_UNBOUND, BINDING_SITE, mutation, artifact, CATH, SCOP
     """
-    type: FeaturesType
-    """
-
-    Numerical value associated with the feature
-
-    Examples:
-    null, null
-    """
+    type: Type
+    "Numerical value associated with the feature"
     value: Float
 }
 
-type FeaturesAdditionalProperties {
-    """
-
-    The additional property name.
-
-    Examples:
-    PARENT_COMP_ID, CATH_NAME, PARTNER_BOND_DISTANCE
-    """
-    property_name: FeaturesAdditionalPropertiesPropertyName
-    property_value: [ObjectScalar]
-}
-
-type FeaturesFeaturePositions {
-    """
-
-    Index at which this segment of the feature begins on the original provenance_source. When reference and source point to the same reference system this file will be null
-
-    Examples:
-    null, null
-    """
+type FeaturePosition {
+    "Index at which this segment of the feature begins on the original provenance_source. When reference and source point to the same reference system this file will be null"
     beg_ori_id: Int
-    """
-
-    Index at which this segment of the feature begins
-
-    Examples:
-    null, null
-    """
+    "Index at which this segment of the feature begins"
     beg_seq_id: Int
-    """
-
-    Index at which this segment of the feature ends on the original provenance_source. If the positional feature maps to a single residue this field will be null. When reference and source point to the same reference system this file will be null
-
-    Examples:
-    null, null
-    """
+    "Index at which this segment of the feature ends on the original provenance_source. If the positional feature maps to a single residue this field will be null. When reference and source point to the same reference system this file will be null"
     end_ori_id: Int
-    """
-
-    Index at which this segment of the feature ends. If the positional feature maps to a single residue this field will be null
-
-    Examples:
-    null, null
-    """
+    "Index at which this segment of the feature ends. If the positional feature maps to a single residue this field will be null"
     end_seq_id: Int
-    """
-
-    Flag that indicates the feature begins before the feature index begin
-
-    Examples:
-    null, null
-    """
+    "Flag that indicates the feature begins before the feature index begin"
     open_begin: Boolean
-    """
-
-    Flag that indicates the feature end after the feature index end
-
-    Examples:
-    null, null
-    """
+    "Flag that indicates the feature end after the feature index end"
     open_end: Boolean
-    """
-
-    Fragment identifier that groups a set of ranges resulting from gaps
-
-    Examples:
-    range-1, range-2
-    """
+    "Fragment identifier that groups a set of ranges resulting from gaps"
     range_id: String
-    """
-
-    The value for the feature at this region
-
-    Examples:
-    null, null, null
-    """
+    "The value for the feature at this region"
     value: Float
     "The value(s) for the feature at this region"
     values: [Float]
 }
 
+"Information about pagination in a connection."
+type PageInfo {
+    "When paginating forwards, the cursor to continue."
+    endCursor: String
+    "When paginating forwards, are there more items?"
+    hasNextPage: Boolean!
+    "When paginating backwards, are there more items?"
+    hasPreviousPage: Boolean!
+    "When paginating backwards, the cursor to continue."
+    startCursor: String
+}
+
 "Query root"
 type Query {
     "Get sequence alignments"
-    alignments(
+    alignment(
         "Query sequence database"
-        from: SequenceReference!,
+        from: SequenceReference,
         "Database sequence identifier"
         queryId: String!,
-        "Optional integer list (2-tuple) to filter alignments to a particular region"
-        range: [Int!],
+        "Optional integer list (2-tuple) to filter the alignments to a particular region"
+        range: [Int],
         "Target Sequence database"
-        to: SequenceReference!
-    ): SequenceAlignments
-    "Get sequence annotations"
+        to: SequenceReference
+    ): AlignmentResponse
+    "Get positional features"
     annotations(
-        "Optional annotation filter by type or target identifier"
-        filters: [AnnotationFilterInput!],
-        "Database sequence identifier"
+        "Optional list of filters that can be used to select what annotations will be retrieved"
+        filters: [FilterInput],
+        "Database entry for whom the annotations will be requested"
         queryId: String!,
-        "Optional integer list (2-tuple) to filter annotations to a particular region"
-        range: [Int!],
-        "Query sequence database"
-        reference: SequenceReference!,
+        "Optional integer list (2-tuple) to filter annotations that fall in a particular region"
+        range: [Int],
+        "Query database"
+        reference: SequenceReference,
         "List defining the annotation collections to be requested"
-        sources: [AnnotationReference]!
-    ): [SequenceAnnotations]
-    "Get group alignments"
-    group_alignments(
-        "Optional string list of allowed group member identifiers"
-        filter: [String!],
-        "Target Sequence database"
+        sources: [Source]
+    ): [AnnotationFeatures]
+    "Get group sequence alignments"
+    group_alignment(
+        "List of allowed PDB entities"
+        filter: [String],
+        "Group Type"
         group: GroupReference!,
-        "Database group identifier"
-        groupId: String!
-    ): SequenceAlignments
-    "Get group annotations"
+        "Group Id"
+        groupId: String
+    ): AlignmentResponse
+    "Get group positional features"
     group_annotations(
-        "Optional annotation filter by type or target identifier"
-        filters: [AnnotationFilterInput!],
-        "Query sequence database"
+        "Optional list of filters that can be used to select what annotations will be retrieved"
+        filters: [FilterInput],
+        "Group Type"
         group: GroupReference!,
-        "Database sequence identifier"
+        "Group Id"
         groupId: String!,
         "List defining the annotation collections to be requested"
-        sources: [AnnotationReference]!
-    ): [SequenceAnnotations]
-    "Get a positional summary of group annotations"
-    group_annotations_summary(
-        "Optional annotation filter by type or target identifier"
-        filters: [AnnotationFilterInput!],
-        "Query sequence database"
-        group: GroupReference!,
-        "Database sequence identifier"
-        groupId: String!,
+        histogram: Boolean,
         "List defining the annotation collections to be requested"
-        sources: [AnnotationReference]!
-    ): [SequenceAnnotations]
-}
-
-type SequenceAlignments {
-    alignment_length: Int
-    alignment_logo: [[AlignmentLogo]]
-    query_sequence: String
-    "Multiple sequence alignment of group members."
-    target_alignments(first: Int, offset: Int): [TargetAlignments]
-}
-
-type SequenceAnnotations {
-    "List of positional features"
-    features: [Features]
-    source: AnnotationReference
-    """
-
-    Database identifier associated to the annotation
-
-    Examples:
-    101M_1, 2UZI.C, P01112
-    """
-    target_id: String
-    target_identifiers: TargetIdentifiers
+        sources: [Source]
+    ): [AnnotationFeatures]
 }
 
-"Subscription root"
-type Subscription {
-    "Get sequence alignments"
-    alignments_subscription(
-        "Query sequence database"
-        from: SequenceReference!,
-        "Database sequence identifier"
-        queryId: String!,
-        "Optional integer list (2-tuple) to filter alignments to a particular region"
-        range: [Int!],
-        "Target Sequence database"
-        to: SequenceReference!
-    ): TargetAlignments
-    "Get sequence annotations"
-    annotations_subscription(
-        "Optional annotation filter by type or target identifier"
-        filters: [AnnotationFilterInput!],
-        "Database sequence identifier"
-        queryId: String!,
-        "Optional integer list (2-tuple) to filter annotations to a particular region"
-        range: [Int!],
-        "Query sequence database"
-        reference: SequenceReference!,
-        "List defining the annotation collections to be requested"
-        sources: [AnnotationReference]!
-    ): SequenceAnnotations
-    "Get group alignments"
-    group_alignments_subscription(
-        "Optional string list of allowed group member identifiers"
-        filter: [String!],
-        "Target Sequence database"
-        group: GroupReference!,
-        "Database group identifier"
-        groupId: String!
-    ): TargetAlignments
-    "Get group annotations"
-    group_annotations_subscription(
-        "Optional annotation filter by type or target identifier"
-        filters: [AnnotationFilterInput!],
-        "Query sequence database"
-        group: GroupReference!,
-        "Database sequence identifier"
-        groupId: String!,
-        "List defining the annotation collections to be requested"
-        sources: [AnnotationReference]!
-    ): SequenceAnnotations
-}
-
-type TargetAlignments {
-    aligned_regions: [AlignedRegions]
+type TargetAlignment {
+    "Aligned region"
+    aligned_regions: [AlignedRegion]
+    "Alignment scores"
     coverage: Coverage
+    "integer that identifies the DNA strand of genome alignments (1 positive strand / -1 negative strand)"
     orientation: Int
+    "Database identifier of the target"
     target_id: String
+    "Full sequence of the target"
     target_sequence: String
 }
 
-type TargetIdentifiers {
-    """
+"A connection to a list of items."
+type TargetAlignmentConnection {
+    "a list of edges"
+    edges: [TargetAlignmentEdge]
+    "details about this specific page"
+    pageInfo: PageInfo!
+}
 
-    This item references an assembly in core_assembly
+"An edge in a connection"
+type TargetAlignmentEdge {
+    "cursor marks a unique position or index into the connection"
+    cursor: String!
+    "The item at the end of the edge"
+    node: TargetAlignment
+}
 
-    Examples:
-    1, 2
-    """
+type TargetIdentifiers {
     assembly_id: String
-    """
-
-    This item references an instance in core_polymer_entity_instance
-
-    Examples:
-    A, B, 1, 2
-    """
     asym_id: String
-    """
-
-    This item references an entity in core_polymer_entity
-
-    Examples:
-    1, 2
-    """
     entity_id: String
-    """
-
-    This item references an entry in core_entry
-
-    Examples:
-    101M, 1ACB
-    """
     entry_id: String
-    """
-
-    This item references an interface in core_interface
-
-    Examples:
-    1, 2
-    """
     interface_id: String
-    """
-
-    This item references a partner of an interface in core_interface
-
-    Examples:
-    null, null
-    """
     interface_partner_index: Int
-    """
-
-    Database identifier associated to the annotation
-
-    Examples:
-    101M_1, 2UZI.C, P01112
-    """
     target_id: String
-    """
-
-    This item references a UniProt document in core_uniprot
-
-    Examples:
-    P01112
-    """
     uniprot_id: String
 }
 
-enum AnnotationReference {
-    PDB_ENTITY
-    PDB_INSTANCE
-    PDB_INTERFACE
-    UNIPROT
+enum GroupReference {
+    matching_uniprot_accession
+    sequence_identity
 }
 
-enum FeaturesAdditionalPropertiesPropertyName {
+enum PropertyName {
     CARD_MODEL_DESCRIPTION
     CARD_MODEL_ORGANISM
     CATH_DOMAIN_ID
@@ -464,11 +250,25 @@ enum FeaturesAdditionalPropertiesPropertyName {
     SHEET_SENSE
     STRAIN_ID
     SUBTYPE
-    TARGET_ID
     WILD_TYPE
 }
 
-enum FeaturesType {
+enum SequenceReference {
+    NCBI_GENOME
+    NCBI_PROTEIN
+    PDB_ENTITY
+    PDB_INSTANCE
+    UNIPROT
+}
+
+enum Source {
+    PDB_ENTITY
+    PDB_INSTANCE
+    PDB_INTERFACE
+    UNIPROT
+}
+
+enum Type {
     ACTIVE_SITE
     ANGLE_OUTLIER
     ARTIFACT
@@ -515,9 +315,6 @@ enum FeaturesType {
     INITIATOR_METHIONINE
     INTRAMEMBRANE_REGION
     IONIC_INTERACTION
-    LIGAND_COVALENT_LINKAGE
-    LIGAND_INTERACTION
-    LIGAND_METAL_COORDINATION_LINKAGE
     LIPID_MOIETY_BINDING_REGION
     MA_QA_METRIC_LOCAL_TYPE_CONTACT_PROBABILITY
     MA_QA_METRIC_LOCAL_TYPE_DISTANCE
@@ -591,35 +388,25 @@ enum FeaturesType {
     ZINC_FINGER_REGION
 }
 
-enum FieldName {
-    TARGET_ID
-    TYPE
-}
-
-enum GroupReference {
-    MATCHING_UNIPROT_ACCESSION
-    SEQUENCE_IDENTITY
+enum fieldName {
+    target_id
+    type
 }
 
-enum OperationType {
-    CONTAINS
-    EQUALS
-}
-
-enum SequenceReference {
-    NCBI_GENOME
-    NCBI_PROTEIN
-    PDB_ENTITY
-    PDB_INSTANCE
-    UNIPROT
+enum operationType {
+    contains
+    equals
 }
 
 "Built-in scalar for dynamic values"
 scalar ObjectScalar
 
-input AnnotationFilterInput {
-    field: FieldName!
-    operation: OperationType!
-    source: AnnotationReference
-    values: [String!]!
+"Use SPQR's SchemaPrinter to remove this from SDL"
+scalar UNREPRESENTABLE
+
+input FilterInput {
+    field: fieldName
+    operation: operationType
+    source: Source
+    values: [String]
 }

package/lib/RcsbQueries/QueryCheck.js

@@ -15,4 +15,3 @@ validateQueries(configYosemiteGraphQL.schema, configYosemiteGraphQL.documents).t
     console.error("DATA API failed");
     console.error(e);
 });
-//# sourceMappingURL=QueryCheck.js.map

package/lib/RcsbRequest/RcsbRequestClient.js

@@ -5,4 +5,3 @@ export const rcsbRequestClient = {
     yosemite: new GraphQLRequest("data-api"),
     arches: new SearchRequest()
 };
-//# sourceMappingURL=RcsbRequestClient.js.map

package/lib/RcsbRequest/RcsbRequestContextManager.d.ts

@@ -9,7 +9,7 @@ import { EntryPropertyInterface } from "../RcsbCollectTools/DataCollectors/Multi
 import { FacetType } from "../RcsbSeacrh/FacetStore/FacetMemberInterface";
 import { ReturnType } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchEnums";
 import { ResultsContentType, SearchQuery } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
-import { RequestConfig as GraphqlRequestInit } from "graphql-request/build/esm/types";
+import { RequestConfig as GraphqlRequestInit } from "graphql-request/src/types";
 import { PolymerEntityInterface } from "../RcsbCollectTools/DataCollectors/MultiplePolymerEntityCollector";
 import { InstanceSequenceInterface } from "../RcsbCollectTools/DataCollectors/MultipleInstanceSequencesCollector";
 import { SearchQueryType } from "@rcsb/rcsb-search-tools/lib/SearchQueryTools/SearchQueryInterfaces";

package/lib/RcsbRequest/RcsbRequestContextManager.js

@@ -151,4 +151,3 @@ class RcsbRequestContextManager {
     }
 }
 export const rcsbRequestCtxManager = new RcsbRequestContextManager();
-//# sourceMappingURL=RcsbRequestContextManager.js.map