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sources.js
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sources.js
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/* eslint-disable no-use-before-define */
const AWS = require("aws-sdk");
const {fetch} = require("./fetch");
const queryString = require("query-string");
const {NoDatasetPathError, InvalidSourceImplementation} = require("./exceptions");
const utils = require("./utils");
const S3 = new AWS.S3();
/* These Source, Dataset, and Narrative classes contain information to map an
* array of dataset/narrative path parts onto a URL. Source selection and
* dataset path aliasing (/flu → /flu/seasonal/h3n2/ha/3y) is handled in
* getDatasetHelpers.parsePrefix().
*
* The class definitions would be a bit shorter/prettier if we were using Babel
* to allow class properties on Node.
*/
class Source {
static get _name() {
throw new InvalidSourceImplementation("_name() must be implemented by subclasses");
}
get name() {
return this.constructor._name;
}
get baseUrl() {
throw new InvalidSourceImplementation("baseUrl() must be implemented by subclasses");
}
static isGroup() { /* is the source a "nextstrain group"? */
return false;
}
dataset(pathParts) {
return new Dataset(this, pathParts);
}
narrative(pathParts) {
return new Narrative(this, pathParts);
}
availableDatasets() {
return [];
}
availableNarratives() {
return [];
}
/* Static access control for this entire source, regardless of any
* instance-specific parameters.
*/
static visibleToUser(user) { // eslint-disable-line no-unused-vars
return true;
}
/* Instance-specific access control delegates to the static method by
* default.
*/
visibleToUser(user) {
return this.constructor.visibleToUser(user);
}
async getInfo() {
throw new InvalidSourceImplementation("getInfo() must be implemented by subclasses");
}
}
class Dataset {
constructor(source, pathParts) {
this.source = source;
this.pathParts = pathParts;
// Require baseParts, otherwise we have no actual dataset path. This
// inspects baseParts because some of the pathParts (above) may not apply,
// which each Dataset subclass determines for itself.
if (!this.baseParts.length) {
throw new NoDatasetPathError();
}
}
get baseParts() {
return this.pathParts.slice();
}
baseNameFor(type) {
const baseName = this.baseParts.join("_");
return type === "main"
? `${baseName}.json`
: `${baseName}_${type}.json`;
}
urlFor(type) {
const url = new URL(this.baseNameFor(type), this.source.baseUrl);
return url.toString();
}
get isRequestValidWithoutDataset() {
return false;
}
}
class Narrative {
constructor(source, pathParts) {
this.source = source;
this.pathParts = pathParts;
}
get baseParts() {
return this.pathParts.slice();
}
get baseName() {
const baseName = this.baseParts.join("_");
return `${baseName}.md`;
}
url() {
const url = new URL(this.baseName, this.source.baseUrl);
return url.toString();
}
}
class CoreSource extends Source {
static get _name() { return "core"; }
get baseUrl() { return "http://data.nextstrain.org/"; }
get repo() { return "nextstrain/narratives"; }
get branch() { return "master"; }
narrative(pathParts) {
return new CoreNarrative(this, pathParts);
}
// The computation of these globals should move here.
availableDatasets() {
return global.availableDatasets[this.name] || [];
}
async availableNarratives() {
const qs = queryString.stringify({ref: this.branch});
const response = await fetch(`https://api.github.com/repos/${this.repo}/contents?${qs}`);
if (response.status !== 200 && response.status !== 304) {
utils.warn(`Error fetching available narratives from GitHub for source ${this.name}`, await utils.responseDetails(response));
return [];
}
const files = await response.json();
return files
.filter((file) => file.type === "file")
.filter((file) => file.name !== "README.md")
.filter((file) => file.name.endsWith(".md"))
.map((file) => file.name
.replace(/[.]md$/, "")
.split("_")
.join("/"));
}
}
class CoreStagingSource extends CoreSource {
static get _name() { return "staging"; }
get baseUrl() { return "http://staging.nextstrain.org/"; }
get repo() { return "nextstrain/narratives"; }
get branch() { return "staging"; }
}
class CoreNarrative extends Narrative {
url() {
const repoBaseUrl = `https://raw.githubusercontent.com/${this.source.repo}/${this.source.branch}/`;
const url = new URL(this.baseName, repoBaseUrl);
return url.toString();
}
}
class CommunitySource extends Source {
constructor(owner, repoName) {
super();
// The GitHub owner and repo names are required.
if (!owner) throw new Error(`Cannot construct a ${this.constructor.name} without an owner`);
if (!repoName) throw new Error(`Cannot construct a ${this.constructor.name} without a repoName`);
this.owner = owner;
[this.repoName, this.branch] = repoName.split(/@/, 2);
if (!this.repoName) throw new Error(`Cannot construct a ${this.constructor.name} without a repoName after splitting on /@/`);
if (!this.branch) {
this.branch = "master";
}
}
static get _name() { return "community"; }
get repo() { return `${this.owner}/${this.repoName}`; }
get baseUrl() { return `https://raw.githubusercontent.com/${this.repo}/${this.branch}/`; }
get repoNameWithBranch() {
return this.branch === "master"
? this.repoName
: `${this.repoName}@${this.branch}`;
}
dataset(pathParts) {
return new CommunityDataset(this, pathParts);
}
narrative(pathParts) {
return new CommunityNarrative(this, pathParts);
}
async availableDatasets() {
const qs = queryString.stringify({ref: this.branch});
const response = await fetch(`https://api.github.com/repos/${this.repo}/contents/auspice?${qs}`);
if (response.status !== 200 && response.status !== 304) {
utils.warn(`Error fetching available datasets from GitHub for source ${this.name}`, await utils.responseDetails(response));
return [];
}
const filenames = (await response.json())
.filter((file) => file.type === "file")
// remove anything which doesn't start with the repo name, which is required of community datasets
.filter((file) => file.name.startsWith(this.repoName))
.map((file) => file.name);
const pathnames = utils.getDatasetsFromListOfFilenames(filenames)
// strip out the repo name from the start of the pathnames
// as CommunityDataset().baseParts will add this in
.map((pathname) => pathname.replace(`${this.repoName}/`, ""));
return pathnames;
}
async availableNarratives() {
const qs = queryString.stringify({ref: this.branch});
const response = await fetch(`https://api.github.com/repos/${this.repo}/contents/narratives?${qs}`);
if (response.status !== 200 && response.status !== 304) {
if (response.status !== 404) {
// not found doesn't warrant an error print, it means there are no narratives for this repo
utils.warn(`Error fetching available narratives from GitHub for source ${this.name}`, await utils.responseDetails(response));
}
return [];
}
const files = await response.json();
return files
.filter((file) => file.type === "file")
.filter((file) => file.name !== "README.md")
.filter((file) => file.name.endsWith(".md"))
.filter((file) => file.name.startsWith(this.repoName))
.map((file) => file.name
.replace(this.repoName, "")
.replace(/^_/, "")
.replace(/[.]md$/, "")
.split("_")
.join("/"));
}
async getInfo() {
/* could attempt to fetch a certain file from the repository if we want to implement
this functionality in the future */
const githubUrl = `https://github.com/${this.owner}/${this.repoName}/tree/${this.branch}`;
return {
title: `${this.owner}'s "${this.repoName}" Nextstrain community build`,
byline: `
Nextstrain community builds are fetched directly from GitHub
repositories, in this case ${githubUrl}. The available datasets and
narratives in this repository are listed below.
`,
showDatasets: true,
showNarratives: true,
/* avatar could be fetched here & sent in base64 or similar, or a link sent. The former (or similar) has the advantage
of private S3 buckets working, else the client will have to make (a) an authenticated request (too much work)
or (b) a subsequent request to nextstrain.org/charon (why not do it at once?) */
avatar: `https://github.com/${this.owner}.png?size=200`
};
}
}
class CommunityDataset extends Dataset {
get baseParts() {
// We require datasets are in the auspice/ directory and include the repo
// name in the file basename.
return [`auspice/${this.source.repoName}`, ...this.pathParts];
}
get isRequestValidWithoutDataset() {
if (!this.pathParts.length) {
return true;
}
return false;
}
}
class CommunityNarrative extends Narrative {
get baseParts() {
// We require narratives are in the narratives/ directory and include the
// repo name in the file basename.
return [`narratives/${this.source.repoName}`, ...this.pathParts];
}
}
class S3Source extends Source {
get bucket() {
throw new InvalidSourceImplementation("bucket() must be implemented by subclasses");
}
get baseUrl() {
return `https://${this.bucket}.s3.amazonaws.com`;
}
async _listObjects() {
// XXX TODO: This will only return the first 1000 objects. That's fine for
// now (for comparison, nextstrain-data only has ~500), but we really
// should iterate over the whole bucket contents using the S3 client's
// pagination support.
// -trs, 30 Aug 2019
const list = await S3.listObjectsV2({Bucket: this.bucket}).promise();
return list.Contents;
}
async availableDatasets() {
const objects = await this._listObjects();
const pathnames = utils.getDatasetsFromListOfFilenames(objects.map((object) => object.Key));
return pathnames;
}
async availableNarratives() {
// Walking logic borrowed from auspice's cli/server/getAvailable.js
const objects = await this._listObjects();
return objects
.map((object) => object.Key)
.filter((file) => file.endsWith(".md"))
.map((file) => file
.replace(/[.]md$/, "")
.split("_")
.join("/"));
}
/**
* Get information about a (particular) source.
* The data could be a JSON, or a markdown with YAML frontmatter. Or something else.
* This is very similar to our previous discussions around moving the auspice footer
* content to the dataset JSON - it would be nice to allow links etc to be written in
* the title/byline. One advantage of this being outside of the auspice codebase is that
* we can iterate on it after pushing live to nextstrain.org
*/
async getInfo() {
try {
/* attempt to fetch customisable information from S3 bucket */
throw new Error();
} catch (err) {
/* Appropriate fallback if no customised data is available */
return {
title: `"${this.name}" Nextstrain group`,
byline: `The available datasets and narratives in this group are listed below.`,
showDatasets: true,
showNarratives: true
};
}
}
}
class PrivateS3Source extends S3Source {
dataset(pathParts) {
return new PrivateS3Dataset(this, pathParts);
}
narrative(pathParts) {
return new PrivateS3Narrative(this, pathParts);
}
static visibleToUser(user) { // eslint-disable-line no-unused-vars
throw new InvalidSourceImplementation("visibleToUser() must be implemented explicitly by subclasses (not inherited from PrivateS3Source)");
}
}
class PrivateS3Dataset extends Dataset {
urlFor(type) {
return S3.getSignedUrl("getObject", {
Bucket: this.source.bucket,
Key: this.baseNameFor(type)
});
}
}
class PrivateS3Narrative extends Narrative {
url() {
return S3.getSignedUrl("getObject", {
Bucket: this.source.bucket,
Key: this.baseName
});
}
}
class PublicGroupSource extends S3Source {
get bucket() { return `nextstrain-${this.name}`; }
static isGroup() {
return true;
}
}
class PrivateGroupSource extends PrivateS3Source {
get bucket() { return `nextstrain-${this.name}`; }
static visibleToUser(user) {
return !!user && !!user.groups && user.groups.includes(this._name);
}
static isGroup() {
return true;
}
}
class BlabSource extends PublicGroupSource {
static get _name() { return "blab"; }
}
class InrbDrcSource extends PrivateGroupSource {
/* Person to contact for enquiries: Alli Black / James Hadfield */
static get _name() { return "inrb-drc"; }
// INRB's bucket is named differently due to early adoption
get bucket() { return "nextstrain-inrb"; }
}
class NzCovid19PrivateSource extends PrivateGroupSource {
/* Person to contact for enquiries: James Hadfield */
static get _name() { return "nz-covid19-private"; }
}
class AllWalesPrivateSource extends PrivateGroupSource {
/* Person to contact for enquiries: James Hadfield */
static get _name() { return "allwales-private"; }
}
class NextspainSource extends PublicGroupSource {
/* Person to contact for enquiries: James Hadfield */
static get _name() { return "nextspain"; }
}
class SeattleFluSource extends PublicGroupSource {
static get _name() { return "seattleflu"; }
}
const sources = [
CoreSource,
CoreStagingSource,
CommunitySource,
/* Public nextstrain groups: */
BlabSource,
SeattleFluSource,
NextspainSource,
/* Private nextstain groups: */
NzCovid19PrivateSource,
AllWalesPrivateSource,
InrbDrcSource
];
const sourceMap = new Map(sources.map(s => [s._name, s]));
utils.verbose("Sources are:", sourceMap);
module.exports = sourceMap;