F get info all genomes (#17)

* initial commmit

* get all genome info

* fixing edge cases

* fixing edge cases

* 1.5.1

* less logs during tests

package.json

@@ -1,6 +1,6 @@
 {
   "name": "node-mist3",
-  "version": "1.5.0",
+  "version": "1.5.1",
   "description": "Helper package to deal with MiST3 API",
   "main": "src/index.js",
   "scripts": {

src/Genomes.js

@@ -20,7 +20,6 @@ class Genomes extends NodeMist3 {
 	getGenomeInfoByVersion(version) {
 		this.httpsOptions.method = 'GET'
 		this.httpsOptions.path = '/v1/genomes/' + version
-		this.httpsOptions.method = 'GET'
 		this.httpsOptions.header = {}
 		return new Promise((resolve, reject) => {
 			this.log.info('Fetching info from genome: ' + version)
@@ -39,4 +38,72 @@ class Genomes extends NodeMist3 {
 			req.end()
 		})
 	}
+
+	getInfoAll() {
+		const self = this
+		const per_page = 100
+		this.httpsOptions.method = 'GET'
+		const getOnePage = (page) => { 
+			self.httpsOptions.path = `/v1/genomes?per_page=${per_page}&page=${page}`
+			const chunks = []
+			return new Promise((resolve, reject) => {
+				const req = https.request(self.httpsOptions, (res) => {
+					if (res.statusCode === 400) {
+						buffer.push(Buffer.from([null]))
+					}
+					if (res.statusCode !== 200) {
+						reject(res.statusMessage)
+					}
+					res.on('data', function(chunk) {
+						chunks.push(chunk)
+					})
+					res.on('end', function() {
+						let newGenes = ''
+						const buffer = Buffer.concat(chunks)
+						try {
+							newGenes = JSON.parse(buffer)
+							resolve(newGenes)
+						}
+						catch(err) {
+							self.log.error(buffer.toString())
+							reject(err)
+						}
+					})
+				})
+				req.end()
+			})	
+		}
+		async function getAll() {
+			const per_page = 100
+			const infoAllGenomes = []
+			let page = 1
+			let maxIterations = 1000
+			let morePages = true
+			while (morePages === true && maxIterations > 0) {
+				self.log.debug(`Requesting page ${page}`)
+				await getOnePage(page).then(function(data) {
+					self.log.debug(`Page ${page} received`)
+					if (data.length !== 0) {
+ 						data.forEach((genome) => {
+							infoAllGenomes.push(genome)
+						})
+						page++
+					}
+					else {
+						morePages = false
+					}
+				})
+				.catch((err) => {
+					morePages = false
+					throw err
+				})
+				maxIterations--
+			}
+			return infoAllGenomes
+		}
+		return getAll().then((allInfo) => {
+			this.log.debug('Done fetching genomes')
+			return allInfo
+		})
+	}
 }

src/Genomes.tests.js

@@ -16,4 +16,14 @@ describe('Genomes', function() {
 			})
 		})
 	})
+	describe('getInfoAll', function() {
+		it('should get info of all genomes', function() {
+			this.timeout(240000)
+			const genomes = new Genomes()
+			const minNumGenomes = 5000
+			return genomes.getInfoAll().then((genomeInfoAll) => {
+				expect(genomeInfoAll.length).greaterThan(minNumGenomes)
+			})
+		})
+	})
 })

src/MakeFasta.js

@@ -49,15 +49,20 @@ class MakeFasta {
 	}
 
 	makeFastaEntry_(gene) {
+		this.log.debug(gene)
 		const header = this.generateTag_(gene)
 		const sequence = this.getSequence_(gene)
 		return '>' + header + '\n' + sequence + '\n'
 	}
 
 	generateTag_(geneInfo) {
-		const genus = this.genomeInfo_.genus
+		this.log.debug(this.genomeInfo_)
+		let genus = this.genomeInfo_.genus
+		if (!genus)
+			genus = this.genomeInfo_.species.split(' ')[0]
+		this.log.debug(genus)
 		const species = this.genomeInfo_.species.split(' ')[1]
-
+		this.log.debug(species)
 		let orgID = genus.substring(0, fastaTagDefaults.numOfLettersForGenus)
 		orgID += fastaTagDefaults.orgIdSeparator
 		orgID += species.substring(0, fastaTagDefaults.numOfLettersForSpecies)

src/MakeFasta.tests.js

@@ -49,6 +49,27 @@ describe('MakeFasta', function() {
 				expect(fastaEntry).eql(expected)
 			})
 		})
+		it('should pass with this gene too', function() {
+			const geneStableId = 'GCF_000224475.1-HALAR_RS01010'
+			const genomeVersion = 'GCF_000224475.1'
+			const expectedFastaEntry = '>ha_arc|GCF_000224475.1-HALAR_RS01010\nMTDQEVQQTNTLRQVDVMVRPTTRFPVPLSDGYSVYSALLGVLEDVDADVSAHIHDSPLGSLHSSGLQGVFGDSDRDYHKTLRPNESYQLRLGVVDPADLDIFQALVNALVLDGDTIELSHGTLQVDRFESVNTTHEDIVTEAGSMDNPTIELSFETATCIEEAGEITTMFPHRGAVFSSLLGKWNRSVSDDLELELDRETIERNVIEKPIARTYNTHSVLVNRVKNKDGETRNLFRQGFTGECSYDFKNASDSVQNAVTALGLFAEYSGVGSAVARGCGCVSAEVAGQ\n'
+			const genomes = new Genomes()
+			const genes = new Genes()
+			return genomes.getGenomeInfoByVersion(genomeVersion).then((genomeInfo) => {
+				const mkFasta = new MakeFasta(genomeInfo)
+				return genes.info(geneStableId)
+					.then((geneInfo) => {
+						return genes.addAseqInfo([geneInfo])
+					})
+					.then((geneInfoPlus) => {
+						console.log(geneInfoPlus)
+						return mkFasta.processOne(geneInfoPlus[0])
+					})
+					.then((fastaEntry) => {
+						expect(fastaEntry).eql(expectedFastaEntry)
+					})
+			})
+		})
 	})
 	describe('processMany', function() {
 		it('should pass', function() {

src/NodeMist3Abstract.tests.js

@@ -10,4 +10,6 @@ const should = chai.should()
 
 const NodeMist3Abstract = require('./NodeMist3Abstract')
 
-describe.skip('NodeMist3Abstract')
+describe('NodeMist3Abstract', function() {
+	it.skip('Find a valid API endpoint')
+})

test/mochabunyan.opts

@@ -1,5 +1,5 @@
 {
     "mute": false,
-    "level": "debug",
+    "level": "warn",
     "reporter": "spec"
 }