bionode-ncbi - npm Package Compare versions

Comparing version 0.1.1 to 0.2.0

lib/bionode-ncbi.js

@@ -36,2 +36,3 @@ // # bionode-ncbi
 var concat = require('concat-stream')
+var pumpify = require('pumpify')
 
@@ -86,9 +87,35 @@
 NCBI.prototype.search = function(db, term, cb) {
-  var stream = through.obj(transform)
+  var xmlProperties = ncbi.XMLPROPERTIES[db]
+
+  var finish
+  if (db === 'sra') {
+    finish = pumpify.obj(
+      tool.ensureIsArray('runs.Run'),
+      tool.filterObjectsArray('total_bases', '', 'runs.Run')
+    )
+  }
+  else {
+    finish = through.obj()
+  }
+
+  var stream = pumpify.obj(
+    _searchURL(db, term),
+    _requestStream(),
+    _dataURL(),
+    _requestStream(),
+    tool.extractProperty('result'),
+    tool.deleteProperty('uids'),
+    tool.arraySplit(),
+    tool.XMLToJSProperties(xmlProperties),
+    finish
+  )
+
   if (term) { stream.write(term); stream.end() }
   if (cb) { stream.pipe(concat(cb)) }
   else { return stream }
+}
 
+function _searchURL(db, term) {
+  var stream = through.obj(transform)
   function transform(obj, enc, next) {
-    var self = this
     var query = [
@@ -101,33 +128,28 @@ ncbi.APIROOT + 'esearch.fcgi?',
     ].join('&')
-
-    var getUIDs = _requestData(db)
-
     debug('esearch request', query)
-
-    var req = request({ uri: query, json: true })
-
-    req.on('response', function(resp) {
-      debug('esearch response', resp.statusCode)
-    })
-
-    req
-    .pipe(JSONStream.parse())
-    .pipe(_requestsSplit(db))
-    .pipe(getUIDs)
-
-    _attachStandardEvents(getUIDs, self, next)
+    this.push(query)
+    next()
   }
+  return stream
 }
 
-function _requestsSplit(db) {
-  return through.obj(transform)
+function _dataURL() {
+  var stream = through.obj(transform)
+  return stream
   function transform(obj, enc, next) {
-    debug('esearch results', obj)
-    var self = this
-    var webenv = obj.esearchresult.webenv
     var count = obj.esearchresult.count
     var numRequests = Math.floor(count / ncbi.RETURNMAX)
     for (var i = 0; i <= numRequests; i++) {
-      var start = { db: db, webenv: webenv, retstart: i * ncbi.RETURNMAX }
-      self.push(start)
+      var retstart = i * ncbi.RETURNMAX
+      var query = [
+        ncbi.APIROOT + 'esummary.fcgi?',
+        ncbi.DEFAULTS,
+        'db=' + obj.db,
+        'query_key=1',
+        'WebEnv=' + obj.esearchresult.webenv,
+        'retmax=' + ncbi.RETURNMAX,
+        'retstart=' + retstart
+      ].join('&')
+      debug('esummary request', query)
+      this.push(query)
     }
@@ -138,46 +160,19 @@ next()
 
-function _requestData(db) {
-  return through.obj(transform)
+function _requestStream() {
+  var stream = through.obj(transform)
+  var outStream = through.obj()
   function transform(obj, enc, next) {
     var self = this
-
-    var query = [
-      ncbi.APIROOT + 'esummary.fcgi?',
-      ncbi.DEFAULTS,
-      'db=' + obj.db,
-      'query_key=1',
-      'WebEnv=' + obj.webenv,
-      'retmax=' + ncbi.RETURNMAX,
-      'retstart=' + obj.retstart
-    ].join('&')
-    var xmlProperties = ncbi.XMLPROPERTIES[db] || []
-
-    var finish = through.obj()
-    if (db === 'sra') {
-      var sraFinish = tool.filterObjectsArray('total_bases', '', 'runs.Run')
-      _attachStandardEvents(sraFinish, self, next)
-      finish
-      .pipe(tool.ensureIsArray('runs.Run'))
-      .pipe(sraFinish)
+    request({ uri: obj, json: true }, gotData)
+    function gotData(err, res, body) {
+      debug('request response', res.statusCode)
+      debug('request results', body)
+      if (body.esearchresult && body.esearchresult.ERROR) {
+        self.emit('error', new Error(body.esearchresult.ERROR))
+      }
+      self.push(body)
+      next()
     }
-    else {
-      _attachStandardEvents(finish, self, next)
-    }
-
-    debug('esummary request', query)
-
-    var req = request({uri: query, json: true})
-
-    req.on('response', function(resp) {
-      debug('esummary response', resp.statusCode)
-    })
-
-    req
-    .pipe(JSONStream.parse())
-    .pipe(tool.extractProperty('result'))
-    .pipe(tool.deleteProperty('uids'))
-    .pipe(tool.arraySplit())
-    .pipe(tool.XMLToJSProperties(xmlProperties))
-    .pipe(finish)
   }
+  return stream
 }
@@ -184,0 +179,0 @@

package.json

 {
   "name": "bionode-ncbi",
   "description": "Node.js module for working with the NCBI API (aka e-utils) using Streams.",
-  "version": "0.1.1",
+  "version": "0.2.0",
   "homepage": "http://github.com/bionode/bionode-ncbi",
@@ -26,3 +26,4 @@ "repository": {
     "xml2js": "^0.4.4",
-    "concat-stream": "~1.4.6"
+    "concat-stream": "~1.4.6",
+    "pumpify": "^1.3.2"
   },
@@ -29,0 +30,0 @@ "devDependencies": {

README.md

@@ -103,5 +103,5 @@ <p align="center">
 [gitter-url]: https://gitter.im/bionode/bionode-ncbi
-[doi-url]: http://dx.doi.org/10.5281/zenodo.11129
-[doi-image]: http://img.shields.io/badge/doi-10.5281/zenodo.11129-blue.svg?style=flat
+[doi-url]: http://dx.doi.org/10.5281/zenodo.11315
+[doi-image]: http://img.shields.io/badge/doi-10.5281/zenodo.11315-blue.svg?style=flat
 
 [![Bitdeli Badge](http://d2weczhvl823v0.cloudfront.net/bionode/bionode-ncbi/trend.png)](https://bitdeli.com/free "Bitdeli Badge")

test/data.json

@@ -35,8 +35,2 @@ {
           "srcUID" : "35533",
-          "destUID" : "5357",
-          "destDB" : "bioproject"
-        },
-        {
-          "srcDB" : "sra",
-          "srcUID" : "35533",
           "destUID" : "53577",
@@ -43,0 +37,0 @@ "destDB" : "bioproject"

test/guillardia-theta.sra.json

 [
-{"uid":"35523","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"19695","total_bases":"5631540","total_size":"13923541","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029662","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712 Whole Genome Sequencing Project"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"FTZB","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Biosample":{"id":"116900","acc":"SAMN00116900","sample_id":"123602","sample_acc":"SRS118433"},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070672","total_spots":"19695","total_bases":"5631540","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":"    ","createdate":"2011/10/29","updatedate":"2010/10/29"}
+{"uid":"35523","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"19695","total_bases":"5631540","total_size":"13923541","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029662","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"FTZB","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Biosample":{"id":"116900","acc":"SAMN00116900","sample_id":"123602","sample_acc":"SRS118433"},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070672","total_spots":"19695","total_bases":"5631540","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":"    ","createdate":"2011/10/29","updatedate":"2010/10/29"}
 ,
-{"uid":"35524","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"204588","total_bases":"58208970","total_size":"146515335","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029663","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712 Whole Genome Sequencing Project"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"FTZB","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Biosample":{"id":"116900","acc":"SAMN00116900","sample_id":"123602","sample_acc":"SRS118433"},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070673","total_spots":"204588","total_bases":"58208970","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":"    ","createdate":"2011/10/29","updatedate":"2010/10/29"}
+{"uid":"35524","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"204588","total_bases":"58208970","total_size":"146515335","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029663","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"FTZB","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Biosample":{"id":"116900","acc":"SAMN00116900","sample_id":"123602","sample_acc":"SRS118433"},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070673","total_spots":"204588","total_bases":"58208970","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":"    ","createdate":"2011/10/29","updatedate":"2010/10/29"}
 ,
-{"uid":"35525","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"295457","total_bases":"85081326","total_size":"216274455","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029664","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712 Whole Genome Sequencing Project"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"FTZB","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Biosample":{"id":"116900","acc":"SAMN00116900","sample_id":"123602","sample_acc":"SRS118433"},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070674","total_spots":"295457","total_bases":"85081326","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":"    ","createdate":"2011/10/29","updatedate":"2010/10/29"}
+{"uid":"35525","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"295457","total_bases":"85081326","total_size":"216274455","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029664","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"FTZB","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Biosample":{"id":"116900","acc":"SAMN00116900","sample_id":"123602","sample_acc":"SRS118433"},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070674","total_spots":"295457","total_bases":"85081326","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":"    ","createdate":"2011/10/29","updatedate":"2010/10/29"}
 ,
-{"uid":"35526","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"11355","total_bases":"2962463","total_size":"7479863","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029665","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712 Whole Genome Sequencing Project"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"FTZC","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Biosample":{"id":"116900","acc":"SAMN00116900","sample_id":"123602","sample_acc":"SRS118433"},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070675","total_spots":"11355","total_bases":"2962463","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":"    ","createdate":"2011/10/29","updatedate":"2010/10/29"}
+{"uid":"35526","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"11355","total_bases":"2962463","total_size":"7479863","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029665","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"FTZC","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Biosample":{"id":"116900","acc":"SAMN00116900","sample_id":"123602","sample_acc":"SRS118433"},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070675","total_spots":"11355","total_bases":"2962463","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":"    ","createdate":"2011/10/29","updatedate":"2010/10/29"}
 ,
-{"uid":"35527","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"286676","total_bases":"72084130","total_size":"191124885","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029666","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712 Whole Genome Sequencing Project"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"FTZC","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Biosample":{"id":"116900","acc":"SAMN00116900","sample_id":"123602","sample_acc":"SRS118433"},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070676","total_spots":"286676","total_bases":"72084130","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":"    ","createdate":"2011/10/29","updatedate":"2010/10/29"}
+{"uid":"35527","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"286676","total_bases":"72084130","total_size":"191124885","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029666","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"FTZC","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Biosample":{"id":"116900","acc":"SAMN00116900","sample_id":"123602","sample_acc":"SRS118433"},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070676","total_spots":"286676","total_bases":"72084130","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":"    ","createdate":"2011/10/29","updatedate":"2010/10/29"}
 ,
-{"uid":"35528","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"971916","total_bases":"513131403","total_size":"1174625556","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029667","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712 Whole Genome Sequencing Project"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"GGAN","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Biosample":{"id":"116900","acc":"SAMN00116900","sample_id":"123602","sample_acc":"SRS118433"},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070677","total_spots":"971916","total_bases":"513131403","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":"    ","createdate":"2011/10/29","updatedate":"2010/10/29"}
+{"uid":"35528","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"971916","total_bases":"513131403","total_size":"1174625556","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029667","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"GGAN","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Biosample":{"id":"116900","acc":"SAMN00116900","sample_id":"123602","sample_acc":"SRS118433"},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070677","total_spots":"971916","total_bases":"513131403","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":"    ","createdate":"2011/10/29","updatedate":"2010/10/29"}
 ,
-{"uid":"35529","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"1131540","total_bases":"588220300","total_size":"1327676112","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029668","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712 Whole Genome Sequencing Project"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"GGAN","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Biosample":{"id":"116900","acc":"SAMN00116900","sample_id":"123602","sample_acc":"SRS118433"},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070678","total_spots":"1131540","total_bases":"588220300","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":"    ","createdate":"2011/10/29","updatedate":"2010/10/29"}
+{"uid":"35529","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"1131540","total_bases":"588220300","total_size":"1327676112","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029668","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"GGAN","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Biosample":{"id":"116900","acc":"SAMN00116900","sample_id":"123602","sample_acc":"SRS118433"},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070678","total_spots":"1131540","total_bases":"588220300","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":"    ","createdate":"2011/10/29","updatedate":"2010/10/29"}
 ,
-{"uid":"35530","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"875108","total_bases":"467593710","total_size":"1055151585","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029669","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712 Whole Genome Sequencing Project"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"GGAN","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Biosample":{"id":"116900","acc":"SAMN00116900","sample_id":"123602","sample_acc":"SRS118433"},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070679","total_spots":"875108","total_bases":"467593710","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":"    ","createdate":"2011/10/29","updatedate":"2010/10/29"}
+{"uid":"35530","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"875108","total_bases":"467593710","total_size":"1055151585","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029669","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"GGAN","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Biosample":{"id":"116900","acc":"SAMN00116900","sample_id":"123602","sample_acc":"SRS118433"},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070679","total_spots":"875108","total_bases":"467593710","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":"    ","createdate":"2011/10/29","updatedate":"2010/10/29"}
 ,
-{"uid":"35531","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"1277503","total_bases":"657634727","total_size":"1479299694","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029670","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712 Whole Genome Sequencing Project"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"GGAN","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Biosample":{"id":"116900","acc":"SAMN00116900","sample_id":"123602","sample_acc":"SRS118433"},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070680","total_spots":"1277503","total_bases":"657634727","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":"    ","createdate":"2011/10/29","updatedate":"2010/10/29"}
+{"uid":"35531","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"1277503","total_bases":"657634727","total_size":"1479299694","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029670","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"GGAN","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Biosample":{"id":"116900","acc":"SAMN00116900","sample_id":"123602","sample_acc":"SRS118433"},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070680","total_spots":"1277503","total_bases":"657634727","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":"    ","createdate":"2011/10/29","updatedate":"2010/10/29"}
 ,
-{"uid":"35532","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"873145","total_bases":"341989978","total_size":"860077955","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029671","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712 Whole Genome Sequencing Project"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"GPNF","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Biosample":{"id":"116900","acc":"SAMN00116900","sample_id":"123602","sample_acc":"SRS118433"},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070681","total_spots":"873145","total_bases":"341989978","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":"    ","createdate":"2011/10/29","updatedate":"2010/10/29"}
+{"uid":"35532","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"873145","total_bases":"341989978","total_size":"860077955","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029671","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"GPNF","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Biosample":{"id":"116900","acc":"SAMN00116900","sample_id":"123602","sample_acc":"SRS118433"},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070681","total_spots":"873145","total_bases":"341989978","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":"    ","createdate":"2011/10/29","updatedate":"2010/10/29"}
 ,
-{"uid":"35533","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"853766","total_bases":"335390762","total_size":"847553880","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029672","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712 Whole Genome Sequencing Project"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"GPNF","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Biosample":{"id":"116900","acc":"SAMN00116900","sample_id":"123602","sample_acc":"SRS118433"},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070682","total_spots":"853766","total_bases":"335390762","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":"    ","createdate":"2011/10/29","updatedate":"2010/10/29"}
+{"uid":"35533","expxml":{"Summary":{"Title":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library.","Platform":{"_":"LS454","instrument_model":"454 GS FLX"},"Statistics":{"total_runs":"1","total_spots":"853766","total_bases":"335390762","total_size":"847553880","load_done":"true","static_data_available":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA025478","center_name":"JGI","contact_name":"Sam Pitluck","lab_name":"PGF"},"Experiment":{"acc":"SRX029672","ver":"1","status":"public","name":"454 sequencing of Guillardia theta CCMP2712 random whole genome shotgun library."},"Study":{"acc":"SRP004020","name":"Guillardia theta CCMP2712"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS118433","name":""},"Instrument":{"LS454":"454 GS FLX"},"Library_descriptor":{"LIBRARY_NAME":"GPNF","LIBRARY_STRATEGY":"WGS","LIBRARY_SOURCE":"GENOMIC","LIBRARY_SELECTION":"RANDOM","LIBRARY_LAYOUT":{"SINGLE":""}},"Biosample":{"id":"116900","acc":"SAMN00116900","sample_id":"123602","sample_acc":"SRS118433"},"Bioproject":"SRP004020"},"runs":{"Run":[{"acc":"SRR070682","total_spots":"853766","total_bases":"335390762","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":"    ","createdate":"2011/10/29","updatedate":"2010/10/29"}
 ,
@@ -24,0 +24,0 @@ {"uid":"333627","expxml":{"Summary":{"Title":"Guillardia theta CCMP2712 Transcriptome","Platform":{"_":"ILLUMINA","instrument_model":"Illumina HiSeq 2000"},"Statistics":{"total_runs":"1","total_spots":"182747799","total_bases":"36549559800","total_size":"22708555668","load_done":"true","cluster_name":"public"}},"Submitter":{"acc":"SRA067334","center_name":"Dalhousie University","contact_name":"Naoko Tanifuji","lab_name":"John Archibald"},"Experiment":{"acc":"SRX242847","ver":"1","status":"public","name":"Guillardia theta CCMP2712 Transcriptome"},"Study":{"acc":"SRP018737","name":"Guillardia theta strain:CCMP2712 Transcriptome or Gene expression"},"Organism":{"taxid":"905079","ScientificName":"Guillardia theta CCMP2712"},"Sample":{"acc":"SRS396737","name":""},"Instrument":{"ILLUMINA":"Illumina HiSeq 2000"},"Library_descriptor":{"LIBRARY_NAME":"","LIBRARY_STRATEGY":"RNA-Seq","LIBRARY_SOURCE":"TRANSCRIPTOMIC","LIBRARY_SELECTION":"cDNA","LIBRARY_LAYOUT":{"PAIRED":{"NOMINAL_LENGTH":"300"}}},"Biosample":{"id":"1923029","acc":"SAMN01923029","sample_id":"474117","sample_acc":"SRS396737"},"Bioproject":"SRP018737"},"runs":{"Run":[{"acc":"SRR747855","total_spots":"182747799","total_bases":"36549559800","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":"    ","createdate":"2014/02/19","updatedate":"2013/02/20"}

No alert changes

Worsened metrics

Total package byte prevSize

439553

decreased by-0.1%

Dependency count

13

increased by8.33%

Lines of code

1367

decreased by-0.15%

Dependency changes

• + Addedpumpify@^1.3.2

• + Addedduplexify@3.7.1(transitive)

• + Addedend-of-stream@1.4.4(transitive)

• + Addedisarray@1.0.0(transitive)

• + Addedonce@1.4.0(transitive)

• + Addedprocess-nextick-args@2.0.1(transitive)

• + Addedpump@2.0.1(transitive)

• + Addedpumpify@1.5.1(transitive)

• + Addedreadable-stream@2.3.8(transitive)

• + Addedsafe-buffer@5.1.2(transitive)

• + Addedstream-shift@1.0.3(transitive)

• + Addedstring_decoder@1.1.1(transitive)

• + Addedutil-deprecate@1.0.2(transitive)

• + Addedwrappy@1.0.2(transitive)

• - Removedsafe-buffer@5.2.1(transitive)