@rcsb/rcsb-saguaro-app 6.0.0-development.1 → 6.0.0-development.3

package/lib/commonjs/RcsbQueries/Borrego/schema.graphql

@@ -0,0 +1,412 @@
+# This file was generated based on ".graphqlconfig". Do not edit manually.
+
+schema {
+    query: Query
+}
+
+type AdditionalProperty {
+    """
+
+    The additional property name.
+
+    Examples:
+    PARENT_COMP_ID, CATH_NAME, PARTNER_BOND_DISTANCE
+    """
+    property_name: PropertyName
+    property_value: [ObjectScalar]
+}
+
+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"
+    target_begin: Int!
+    "Target sequence start position"
+    target_end: Int!
+}
+
+type AlignmentLogo {
+    symbol: String
+    value: 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 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
+}
+
+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
+}
+
+type Feature {
+    additional_properties: [AdditionalProperty]
+    "Free-form text describing the feature"
+    description: String
+    "Identifier of the feature"
+    feature_id: String
+    " 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"
+    provenance_source: String
+    """
+
+    The connection type.
+
+    Examples:
+    ASA_UNBOUND, BINDING_SITE, mutation, artifact, CATH, SCOP
+    """
+    type: Type
+    "Numerical value associated with the feature"
+    value: Float
+}
+
+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"
+    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"
+    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"
+    end_seq_id: Int
+    "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"
+    open_end: Boolean
+    "Fragment identifier that groups a set of ranges resulting from gaps"
+    range_id: String
+    "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"
+    alignment(
+        "Query sequence database"
+        from: SequenceReference,
+        "Database sequence identifier"
+        queryId: String!,
+        "Optional integer list (2-tuple) to filter the alignments to a particular region"
+        range: [Int],
+        "Target Sequence database"
+        to: SequenceReference
+    ): AlignmentResponse
+    "Get positional features"
+    annotations(
+        "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 that fall in a particular region"
+        range: [Int],
+        "Query database"
+        reference: SequenceReference,
+        "List defining the annotation collections to be requested"
+        sources: [Source]
+    ): [AnnotationFeatures]
+    "Get group sequence alignments"
+    group_alignment(
+        "List of allowed PDB entities"
+        filter: [String],
+        "Group Type"
+        group: GroupReference!,
+        "Group Id"
+        groupId: String
+    ): AlignmentResponse
+    "Get group positional features"
+    group_annotations(
+        "Optional list of filters that can be used to select what annotations will be retrieved"
+        filters: [FilterInput],
+        "Group Type"
+        group: GroupReference!,
+        "Group Id"
+        groupId: String!,
+        "List defining the annotation collections to be requested"
+        histogram: Boolean,
+        "List defining the annotation collections to be requested"
+        sources: [Source]
+    ): [AnnotationFeatures]
+}
+
+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
+}
+
+"A connection to a list of items."
+type TargetAlignmentConnection {
+    "a list of edges"
+    edges: [TargetAlignmentEdge]
+    "details about this specific page"
+    pageInfo: PageInfo!
+}
+
+"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
+}
+
+type TargetIdentifiers {
+    assembly_id: String
+    asym_id: String
+    entity_id: String
+    entry_id: String
+    interface_id: String
+    interface_partner_index: Int
+    target_id: String
+    uniprot_id: String
+}
+
+enum GroupReference {
+    matching_uniprot_accession
+    sequence_identity
+}
+
+enum PropertyName {
+    CARD_MODEL_DESCRIPTION
+    CARD_MODEL_ORGANISM
+    CATH_DOMAIN_ID
+    CATH_NAME
+    CLINICAL_SIGNIFICANCE
+    CONSEQUENCE_TYPE
+    DISEASE_TYPE
+    ECOD_DOMAIN_ID
+    ECOD_FAMILY_NAME
+    EVIDENCE
+    LINK
+    MODELCIF_MODEL_ID
+    MUTATED_TYPE
+    OMEGA_ANGLE
+    PARENT_COMP_ID
+    PARTNER_ASYM_ID
+    PARTNER_BOND_DISTANCE
+    PARTNER_COMP_ID
+    PREDICTED_IMPACT
+    SCOP_2_DOMAIN_ID
+    SCOP_2_FAMILY_ID
+    SCOP_2_FAMILY_NAME
+    SCOP_2_SUPERFAMILY_ID
+    SCOP_2_SUPERFAMILY_NAME
+    SCOP_DOMAIN_ID
+    SCOP_NAME
+    SCOP_SUN_ID
+    SHEET_SENSE
+    STRAIN_ID
+    SUBTYPE
+    WILD_TYPE
+}
+
+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
+    ASA
+    ASA_BOUND
+    ASA_UNBOUND
+    BEND
+    BINDING_SITE
+    BOND_OUTLIER
+    CALCIUM_BINDING_REGION
+    CARD_MODEL
+    CATH
+    CHAIN
+    CIS_PEPTIDE
+    COMPOSITIONALLY_BIASED_REGION
+    COVALENT_BOND
+    COVALENT_MODIFICATION_OF_A_NUCLEOTIDE_BASE
+    COVALENT_MODIFICATION_OF_A_NUCLEOTIDE_PHOSPHATE
+    COVALENT_MODIFICATION_OF_A_NUCLEOTIDE_SUGAR
+    COVALENT_RESIDUE_MODIFICATION
+    CROSS_LINK
+    C_MANNOSYLATION_SITE
+    DISORDER
+    DISORDER_BINDING
+    DISULFIDE_BRIDGE
+    DNA_BINDING_REGION
+    DOMAIN
+    ECOD
+    GLYCOSYLATION_SITE
+    HELIX_P
+    HELX_LH_PP_P
+    HELX_RH_3_T_P
+    HELX_RH_AL_P
+    HELX_RH_PI_P
+    HYDROGEN_BOND
+    HYDROPATHY
+    IMGT_ANTIBODY_DESCRIPTION
+    IMGT_ANTIBODY_DOMAIN_NAME
+    IMGT_ANTIBODY_GENE_ALLELE_NAME
+    IMGT_ANTIBODY_ORGANISM_NAME
+    IMGT_ANTIBODY_PROTEIN_NAME
+    IMGT_ANTIBODY_RECEPTOR_DESCRIPTION
+    IMGT_ANTIBODY_RECEPTOR_TYPE
+    INITIATOR_METHIONINE
+    INTRAMEMBRANE_REGION
+    IONIC_INTERACTION
+    LIPID_MOIETY_BINDING_REGION
+    MA_QA_METRIC_LOCAL_TYPE_CONTACT_PROBABILITY
+    MA_QA_METRIC_LOCAL_TYPE_DISTANCE
+    MA_QA_METRIC_LOCAL_TYPE_ENERGY
+    MA_QA_METRIC_LOCAL_TYPE_IPTM
+    MA_QA_METRIC_LOCAL_TYPE_NORMALIZED_SCORE
+    MA_QA_METRIC_LOCAL_TYPE_OTHER
+    MA_QA_METRIC_LOCAL_TYPE_PAE
+    MA_QA_METRIC_LOCAL_TYPE_PLDDT
+    MA_QA_METRIC_LOCAL_TYPE_PLDDT_0_1
+    MA_QA_METRIC_LOCAL_TYPE_PLDDT_ALL_ATOM
+    MA_QA_METRIC_LOCAL_TYPE_PLDDT_ALL_ATOM_0_1
+    MA_QA_METRIC_LOCAL_TYPE_PTM
+    MA_QA_METRIC_LOCAL_TYPE_ZSCORE
+    MEMBRANE_SEGMENT
+    METAL_COORDINATION
+    METAL_ION_BINDING_SITE
+    MISMATCHED_BASE_PAIRS
+    MODIFIED_MONOMER
+    MODIFIED_RESIDUE
+    MOGUL_ANGLE_OUTLIER
+    MOGUL_BOND_OUTLIER
+    MUTAGENESIS_SITE
+    MUTATION
+    NON_CONSECUTIVE_RESIDUES
+    NON_STANDARD_AMINO_ACID
+    NON_TERMINAL_RESIDUE
+    NUCLEOTIDE_PHOSPHATE_BINDING_REGION
+    N_GLYCOSYLATION_SITE
+    O_GLYCOSYLATION_SITE
+    PEPTIDE
+    PFAM
+    PROPEPTIDE
+    PROTEIN_BINDING
+    RAMACHANDRAN_OUTLIER
+    REGION_OF_INTEREST
+    REPEAT
+    ROTAMER_OUTLIER
+    RSCC_OUTLIER
+    RSRZ_OUTLIER
+    SABDAB_ANTIBODY_ANTIGEN_NAME
+    SABDAB_ANTIBODY_HEAVY_CHAIN_SUBCLASS
+    SABDAB_ANTIBODY_LIGHT_CHAIN_SUBCLASS
+    SABDAB_ANTIBODY_LIGHT_CHAIN_TYPE
+    SABDAB_ANTIBODY_NAME
+    SABDAB_ANTIBODY_TARGET
+    SCOP
+    SCOP_2_B_SUPERFAMILY
+    SCOP_2_FAMILY
+    SCOP_2_SUPERFAMILY
+    SEQUENCE_CONFLICT
+    SEQUENCE_VARIANT
+    SHEET
+    SHORT_SEQUENCE_MOTIF
+    SIGNAL_PEPTIDE
+    SITE
+    SPLICE_VARIANT
+    STEREO_OUTLIER
+    STRN
+    S_GLYCOSYLATION_SITE
+    TOPOLOGICAL_DOMAIN
+    TRANSIT_PEPTIDE
+    TRANSMEMBRANE_REGION
+    TURN_TY_1_P
+    UNASSIGNED_SEC_STRUCT
+    UNOBSERVED_ATOM_XYZ
+    UNOBSERVED_RESIDUE_XYZ
+    UNSURE_RESIDUE
+    ZERO_OCCUPANCY_ATOM_XYZ
+    ZERO_OCCUPANCY_RESIDUE_XYZ
+    ZINC_FINGER_REGION
+}
+
+enum fieldName {
+    target_id
+    type
+}
+
+enum operationType {
+    contains
+    equals
+}
+
+"Built-in scalar for dynamic values"
+scalar ObjectScalar
+
+"Use SPQR's SchemaPrinter to remove this from SDL"
+scalar UNREPRESENTABLE
+
+input FilterInput {
+    field: fieldName
+    operation: operationType
+    source: Source
+    values: [String]
+}

package/lib/commonjs/RcsbQueries/QueryCheck.d.ts

@@ -0,0 +1 @@
+export {};

package/lib/commonjs/RcsbQueries/QueryCheck.js

@@ -0,0 +1,20 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const tslib_1 = require("tslib");
+const configBorregoGraphQL = tslib_1.__importStar(require("../RcsbServerConfig/codegen.borrego.json"));
+const configYosemiteGraphQL = tslib_1.__importStar(require("../RcsbServerConfig/codegen.yosemite.json"));
+const GeneratorTools_1 = require("@rcsb/rcsb-api-tools/build/RcsbGraphQL/Generator/GeneratorTools");
+console.info("Testing DATA API");
+(0, GeneratorTools_1.validateQueries)(configYosemiteGraphQL.schema, configYosemiteGraphQL.documents).then(() => {
+    console.log("DATA API request OK");
+    console.info("Testing 1D API");
+    (0, GeneratorTools_1.validateQueries)(configBorregoGraphQL.schema, configBorregoGraphQL.documents).then(() => {
+        console.log("1D API request OK");
+    }).catch(e => {
+        console.error("1D API failed");
+        console.error(e);
+    });
+}).catch(e => {
+    console.error("DATA API failed");
+    console.error(e);
+});

package/lib/commonjs/RcsbQueries/Yosemite/.graphqlconfig

@@ -0,0 +1,15 @@
+{
+  "name": "Untitled GraphQL Schema",
+  "schemaPath": "schema.graphql",
+  "extensions": {
+    "endpoints": {
+      "Default GraphQL Endpoint": {
+        "url": "https://data.rcsb.org/graphql",
+        "headers": {
+          "user-agent": "JS GraphQL"
+        },
+        "introspect": false
+      }
+    }
+  }
+}

package/lib/commonjs/RcsbQueries/Yosemite/QueryAssemblyInterfaces.graphql

@@ -0,0 +1,10 @@
+query QueryAssemblyInterfaces($assembly_ids: [String!]!){
+    assemblies(
+        assembly_ids: $assembly_ids
+    ){
+        rcsb_id
+        interfaces{
+            rcsb_id
+        }
+    }
+}

package/lib/commonjs/RcsbQueries/Yosemite/QueryEntryInstances.graphql

@@ -0,0 +1,51 @@
+query QueryEntryInstance($entry_id: String!){
+    entry(
+        entry_id:$entry_id
+    ){
+        polymer_entities {
+            polymer_entity_instances{
+                rcsb_id
+                polymer_entity{
+                    rcsb_polymer_entity{
+                        pdbx_description
+                        rcsb_polymer_name_combined{
+                            names
+                        }
+                        formula_weight
+                    }
+                    entity_poly{
+                        rcsb_entity_polymer_type
+                        rcsb_sample_sequence_length
+                    }
+                    rcsb_entity_source_organism {
+                        ncbi_scientific_name
+                    }
+                    entry {
+                        rcsb_entry_info{
+                            experimental_method
+                            resolution_combined
+                            molecular_weight
+                            structure_determination_methodology
+                        }
+                    }
+                }
+                rcsb_polymer_entity_instance_container_identifiers{
+                    asym_id
+                    auth_asym_id
+                    entry_id
+                    entity_id
+                    auth_to_entity_poly_seq_mapping
+                }
+            }
+        }
+        assemblies {
+            rcsb_assembly_container_identifiers {
+                assembly_id
+            }
+            pdbx_struct_assembly_gen{
+                asym_id_list
+            }
+
+        }
+    }
+}

package/lib/commonjs/RcsbQueries/Yosemite/QueryGroup.graphql

@@ -0,0 +1,15 @@
+query QueryGroup($group_id: String!){
+    polymer_entity_group(
+        group_id:$group_id
+    ){
+        rcsb_id
+        rcsb_group_info{
+            group_name
+            group_description
+            group_members_granularity
+        }
+        rcsb_group_container_identifiers{
+            group_member_ids
+        }
+    }
+}

package/lib/commonjs/RcsbQueries/Yosemite/QueryInterfaceInstances.graphql

@@ -0,0 +1,18 @@
+query QueryInterfaceInstance($interface_ids: [String!]!){
+    interfaces(
+        interface_ids:$interface_ids
+    ){
+        rcsb_interface_container_identifiers{
+            rcsb_id
+            interface_id
+            assembly_id
+            entry_id
+        }
+        rcsb_interface_partner{
+            interface_partner_identifier{
+                asym_id
+            }
+        }
+        rcsb_interface_operator
+    }
+}

package/lib/commonjs/RcsbQueries/Yosemite/QueryMultipleEntityInstances.graphql

@@ -0,0 +1,39 @@
+query QueryMultipleEntityInstances($entity_ids: [String!]!){
+    polymer_entities(
+        entity_ids:$entity_ids
+    ){
+        polymer_entity_instances{
+            rcsb_id
+            polymer_entity{
+                rcsb_polymer_entity{
+                    pdbx_description
+                    rcsb_polymer_name_combined{
+                        names
+                    }
+                    formula_weight
+                }
+                entity_poly{
+                    rcsb_entity_polymer_type
+                    rcsb_sample_sequence_length
+                }
+                rcsb_entity_source_organism {
+                    ncbi_scientific_name
+                }
+                entry {
+                    rcsb_entry_info{
+                        experimental_method
+                        resolution_combined
+                        structure_determination_methodology
+                    }
+                }
+            }
+            rcsb_polymer_entity_instance_container_identifiers{
+                asym_id
+                auth_asym_id
+                entry_id
+                entity_id
+                auth_to_entity_poly_seq_mapping
+            }
+        }
+    }
+}

package/lib/commonjs/RcsbQueries/Yosemite/QueryMultipleEntriesProperties.graphql

@@ -0,0 +1,30 @@
+query multiple_entries_properties($entry_ids: [String!]!){
+    entries(entry_ids:$entry_ids){
+        rcsb_id
+        polymer_entities {
+            rcsb_id
+            rcsb_entity_source_organism {
+                ncbi_scientific_name
+            }
+            rcsb_polymer_entity_container_identifiers {
+                entity_id
+                rcsb_id
+            }
+            polymer_entity_instances {
+                rcsb_polymer_entity_instance_container_identifiers {
+                    asym_id
+                }
+                rcsb_id
+            }
+        }
+        rcsb_entry_info{
+            experimental_method
+            resolution_combined
+            molecular_weight
+            structure_determination_methodology
+        }
+        struct {
+            title
+        }
+    }
+}

package/lib/commonjs/RcsbQueries/Yosemite/QueryMultipleInstanceSequences.graphql

@@ -0,0 +1,11 @@
+
+query multiple_instance_sequences($instance_ids: [String!]!){
+    polymer_entity_instances(instance_ids:$instance_ids){
+        rcsb_id
+        polymer_entity{
+            entity_poly{
+                pdbx_seq_one_letter_code_can
+            }
+        }
+    }
+}