@rcsb/rcsb-saguaro-app 6.0.0-development.1 → 6.0.0-development.2

package/lib/ExternalResources/NcbiData/NcbiGenomeSequenceData.d.ts

@@ -0,0 +1,7 @@
+import { RcsbFvTrackData } from "@rcsb/rcsb-saguaro/lib/RcsbDataManager/RcsbDataManager";
+import { LocationViewInterface } from "@rcsb/rcsb-saguaro/lib/RcsbBoard/RcsbBoard";
+export declare class NcbiGenomeSequenceData {
+    private static readonly urlPrefix;
+    private static readonly urlSuffix;
+    static update(ncbiId: string, strand: number, reverse: boolean, trackWidth?: number): ((where: LocationViewInterface) => Promise<RcsbFvTrackData>);
+}

package/lib/ExternalResources/NcbiData/NcbiGenomeSequenceData.js

@@ -0,0 +1,65 @@
+import { asyncScheduler } from "rxjs";
+import resource from "../../RcsbServerConfig/web.resources.json";
+export class NcbiGenomeSequenceData {
+    static update(ncbiId, strand, reverse, trackWidth) {
+        let process = null;
+        return (where) => {
+            if (process)
+                process.unsubscribe();
+            return new Promise((resolve, reject) => {
+                const delta = trackWidth ? trackWidth / (where.to - where.from) : 1000 / (where.to - where.from);
+                if (delta > 4) {
+                    let N = 0;
+                    const timeout = 5000;
+                    const getGenomeSequence = () => {
+                        const Http = new XMLHttpRequest();
+                        Http.timeout = timeout;
+                        const url = NcbiGenomeSequenceData.urlPrefix + 'id=' + ncbiId + '&from=' + where.from + '&to=' + where.to + '&strand=' + strand + NcbiGenomeSequenceData.urlSuffix;
+                        Http.open("GET", url);
+                        Http.send();
+                        Http.onloadend = (e) => {
+                            const sequence = Http.responseText.split("\n").slice(1).join("");
+                            if (sequence.length < 1) {
+                                N++;
+                                console.warn("HTTP error while access URL: " + url + " - empty sequence - " + N);
+                                if (N < 4) {
+                                    process = asyncScheduler.schedule(() => {
+                                        getGenomeSequence();
+                                    }, timeout);
+                                }
+                                else {
+                                    reject("HTTP error while access URL: " + url + " - No more attempts after " + N);
+                                }
+                            }
+                            else {
+                                const selectedOption = [{
+                                        begin: where.from,
+                                        label: reverse ? sequence.split("").reverse().join("") : sequence
+                                    }];
+                                resolve(selectedOption);
+                            }
+                        };
+                        Http.onerror = (e) => {
+                            N++;
+                            console.warn("HTTP error while access URL: " + url + " - " + N);
+                            if (N < 4) {
+                                process = asyncScheduler.schedule(() => {
+                                    getGenomeSequence();
+                                }, timeout);
+                            }
+                            else {
+                                reject("HTTP error while access URL: " + url + " - No more attempts after " + N);
+                            }
+                        };
+                    };
+                    getGenomeSequence();
+                }
+                else {
+                    resolve([]);
+                }
+            });
+        };
+    }
+}
+NcbiGenomeSequenceData.urlPrefix = resource.ncbi_genome_sequence.url;
+NcbiGenomeSequenceData.urlSuffix = resource.ncbi_genome_sequence.url_suffix;

package/lib/ExternalResources/NcbiData/NcbiSummary.d.ts

@@ -0,0 +1,24 @@
+export interface ChromosomeMetadataInterface {
+    ncbiId: string;
+    title: string;
+    organism: string;
+    extra: string;
+    taxid: number;
+    length: number;
+    subtype: string;
+    subname: string;
+    uid: number;
+}
+export interface TaxonomyMetadataInterface {
+    scientificname: string;
+    commonname: string;
+    taxid: number;
+    uid: number;
+}
+export declare class NcbiSummary {
+    private static timeout;
+    private static httpTimeout;
+    private static jobTask;
+    static requestChromosomeData(chrId: string): Promise<ChromosomeMetadataInterface>;
+    static requestTaxonomyData(taxId: string): Promise<TaxonomyMetadataInterface>;
+}

package/lib/ExternalResources/NcbiData/NcbiSummary.js

@@ -0,0 +1,81 @@
+import { asyncScheduler } from "rxjs";
+import resource from "../../RcsbServerConfig/web.resources.json";
+//TODO are static attributes/methods safe in this case ?
+//TODO change `XMLHttpRequest` to `fetch`
+export class NcbiSummary {
+    static requestChromosomeData(chrId) {
+        if (NcbiSummary.jobTask)
+            NcbiSummary.jobTask.unsubscribe();
+        const urlPrefix = resource.ncbi_summary_nuccore.url;
+        const urlSuffix = resource.ncbi_summary_nuccore.url_suffix;
+        return new Promise((resolve, reject) => {
+            const recursiveRequest = () => {
+                const url = urlPrefix + chrId + urlSuffix;
+                const Http = new XMLHttpRequest();
+                Http.timeout = NcbiSummary.httpTimeout;
+                Http.open("GET", url);
+                Http.send();
+                Http.onloadend = (e) => {
+                    var _a;
+                    if (Http.responseText.length == 0) {
+                        NcbiSummary.jobTask = asyncScheduler.schedule(() => {
+                            recursiveRequest();
+                        }, NcbiSummary.timeout);
+                    }
+                    else {
+                        const jsonResult = JSON.parse(Http.responseText);
+                        const uid = (_a = jsonResult === null || jsonResult === void 0 ? void 0 : jsonResult.result) === null || _a === void 0 ? void 0 : _a.uids[0];
+                        const out = jsonResult.result[uid];
+                        out.ncbiId = chrId;
+                        resolve(out);
+                    }
+                };
+                Http.onerror = (e) => {
+                    if (NcbiSummary.jobTask)
+                        NcbiSummary.jobTask.unsubscribe();
+                    NcbiSummary.jobTask = asyncScheduler.schedule(() => {
+                        recursiveRequest();
+                    }, NcbiSummary.timeout);
+                };
+            };
+            recursiveRequest();
+        });
+    }
+    static requestTaxonomyData(taxId) {
+        if (NcbiSummary.jobTask)
+            NcbiSummary.jobTask.unsubscribe();
+        const urlPrefix = resource.ncbi_summary_taxonomy.url;
+        const urlSuffix = resource.ncbi_summary_taxonomy.url_suffix;
+        return new Promise((resolve, reject) => {
+            const recursiveRequest = () => {
+                const url = urlPrefix + taxId + urlSuffix;
+                const Http = new XMLHttpRequest();
+                Http.timeout = NcbiSummary.httpTimeout;
+                Http.open("GET", url);
+                Http.send();
+                Http.onloadend = (e) => {
+                    var _a;
+                    if (Http.responseText.length == 0) {
+                        NcbiSummary.jobTask = asyncScheduler.schedule(() => {
+                            recursiveRequest();
+                        }, NcbiSummary.timeout);
+                    }
+                    else {
+                        const jsonResult = JSON.parse(Http.responseText);
+                        const uid = (_a = jsonResult === null || jsonResult === void 0 ? void 0 : jsonResult.result) === null || _a === void 0 ? void 0 : _a.uids[0];
+                        resolve(jsonResult.result[uid]);
+                    }
+                };
+                Http.onerror = (e) => {
+                    NcbiSummary.jobTask = asyncScheduler.schedule(() => {
+                        recursiveRequest();
+                    }, NcbiSummary.timeout);
+                };
+            };
+            recursiveRequest();
+        });
+    }
+}
+NcbiSummary.timeout = 3000;
+NcbiSummary.httpTimeout = 10000;
+NcbiSummary.jobTask = null;

package/lib/RcsbAnnotationConfig/AnnotationConfigInterface.d.ts

@@ -0,0 +1,66 @@
+import { RcsbFvDisplayTypes } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvDefaultConfigValues";
+import { RcsbFvColorGradient } from "@rcsb/rcsb-saguaro/lib/RcsbDataManager/RcsbDataManager";
+export interface AnnotationConfigInterface {
+    provenance_color_code: {
+        external: string;
+        rcsb_pdb: string;
+        rcsb_link: string;
+        csm: string;
+    };
+    merge?: Array<{
+        merged_types: Array<string>;
+        type: string;
+        title: string;
+        display: RcsbFvDisplayTypes;
+    }>;
+    external_data_order?: Array<string>;
+    instance_order?: Array<string>;
+    entity_order?: Array<string>;
+    config: Array<RcsbAnnotationConfigInterface>;
+}
+export interface RcsbAnnotationConfigInterface {
+    type: string;
+    display: RcsbFvDisplayTypes;
+    color?: string | RcsbFvColorGradient;
+    title: string;
+    prefix?: string;
+    provenanceList: Set<string>;
+    height?: number;
+    key?: string;
+    addToType?: string[];
+    transformToNumerical?: boolean;
+    domain?: [number, number];
+    displayCooccurrence?: boolean;
+    ignore?: boolean;
+    fitTitleWidth?: boolean;
+}
+export interface RcsbDistributionConfigInterface {
+    blockConfig: RcsbTrackBlockConfigInterface[];
+    trackConfig: RcsbTrackConfigInterface[];
+}
+export interface RcsbTrackBlockConfigInterface {
+    type: string;
+    title: string;
+    trackType: string[];
+    sort: string[];
+    contentType: "binary" | "numerical";
+    undefTrack?: {
+        label: string;
+        color: string;
+        id: string;
+    };
+    axisLabel?: string;
+}
+export interface RcsbTrackConfigInterface {
+    type: string;
+    color?: string;
+    label?: string;
+    numericalCategories?: {
+        thresholds: number[];
+        categories: {
+            label: string;
+            color: string;
+            id: string;
+        }[];
+    };
+}

package/lib/RcsbAnnotationConfig/AnnotationConfigInterface.js

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

package/lib/RcsbAnnotationConfig/GroupAnnotationConfig.ac.json

@@ -0,0 +1,98 @@
+{
+    "provenance_color_code": {
+        "external": "#DB9128",
+        "rcsb_pdb": "#325880",
+        "rcsb_link": "#5e94c3",
+        "csm": "#1abdcf"
+    },
+    "config": [{
+            "type": "UNOBSERVED_RESIDUE_XYZ",
+            "title": "UNMODELED RESIDUE",
+            "color": {
+                "colors": "#999999",
+                "thresholds": [0.25, 0.5, 0.75]
+            },
+            "display": "block-area",
+            "transformToNumerical": true
+        }, {
+            "type": "BINDING_SITE",
+            "color": {
+                "colors": "#984657",
+                "thresholds": [0.25, 0.5, 0.75]
+            },
+            "title": "BINDING SITE",
+            "key": "name",
+            "display": "block-area",
+            "fitTitleWidth": true,
+            "transformToNumerical": true
+        }, {
+            "type": "HELIX_P",
+            "color": {
+                "colors": "#e43372",
+                "thresholds": [0.25, 0.5, 0.75]
+            },
+            "title": "HELIX",
+            "display": "block-area",
+            "transformToNumerical": true
+        }, {
+            "type": "SHEET",
+            "color": {
+                "colors": "#f1d23b",
+                "thresholds": [0.25, 0.5, 0.75]
+            },
+            "title": "BETA STRAND",
+            "display": "block-area",
+            "transformToNumerical": true
+        }, {
+            "type": "CATH",
+            "title": "CATH",
+            "color": {
+                "colors": "#e4ad56",
+                "thresholds": [0.25, 0.5, 0.75]
+            },
+            "display": "block-area",
+            "key": "name",
+            "transformToNumerical": true
+        }, {
+            "type": "SCOP",
+            "title": "SCOP",
+            "color": {
+                "colors": "#455d5a",
+                "thresholds": [0.25, 0.5, 0.75]
+            },
+            "display": "block-area",
+            "key": "name",
+            "transformToNumerical": true
+        }, {
+            "type": "PFAM",
+            "title": "PFAM",
+            "color": {
+                "colors": "#ecaca6",
+                "thresholds": [0.25, 0.5, 0.75]
+            },
+            "display": "block-area",
+            "key": "name",
+            "transformToNumerical": true
+        }, {
+            "type": "PROTEIN_BINDING",
+            "title": "PROTEIN BINDING",
+            "color": {
+                "colors": "#33e472",
+                "thresholds": [0.01, 0.25, 0.5, 0.75]
+            },
+            "display": "block-area",
+            "transformToNumerical": true
+        }],
+    "external_data_order": [
+        "CATH",
+        "SCOP",
+        "PFAM"
+    ],
+    "instance_order": [
+        "PROTEIN_BINDING",
+        "HELIX_P",
+        "SHEET",
+        "UNOBSERVED_RESIDUE_XYZ",
+        "BINDING_SITE"
+    ]
+}