update ncbi query

Author: Miachol

api/cmd/ncbi.go

@@ -54,9 +54,7 @@ func init() {
 	setGlobalFlag(ncbiCmd, &BapiClis)
 	ncbiCmd.Flags().StringVarP(&ncbiClis.NcbiDB, "db", "d", "pubmed", "Db specifies the database to search")
 	ncbiCmd.Flags().IntVarP(&ncbiClis.NcbiRetmax, "per-size", "m", 100, "Retmax specifies the number of records to be retrieved per request.")
-	//ncbiCmd.Flags().StringVarP(&ncbiClis.NcbiKeywords, "keywords", "w", "algorithm, tool, model, pipleline, method, database, workflow, dataset, bioinformatics, sequencing, http, github.com, gitlab.com, bitbucket.org", "Keywords to extracted from abstract.")
 	ncbiCmd.Flags().IntVarP(&BapiClis.Thread, "thread", "t", 2, "Thread to process.")
-	//ncbiCmd.Flags().BoolVarP(&BapiClis.CallCor, "call-cor", "", false, "Wheather to calculate the corelated keywords, and return the sentence contains >=2 keywords.")
 	ncbiCmd.Flags().StringVarP(&BapiClis.Email, "email", "e", "[email protected]", "Email specifies the email address to be sent to the server (NCBI website is required).")
 
 	ncbiCmd.Example = `  # query pubmed with 'B-ALL'

api/fetch/ncbi.go

@@ -27,8 +27,11 @@ func Ncbi(BapiClis *types.BapiClisT, ncbiClis *types.NcbiClisT) {
 		log.Fatalf("error: %v\n", err)
 	}
 	log.Infof("Available retrieve %d records.", s.Count)
+	if s.Count == 0 {
+		return
+	}
 	from, end := cnet.SetQueryFromEnd(BapiClis.From, BapiClis.Size, s.Count)
-	log.Infof("Will retrieve %d records, from %d to %d.", end-from+1, from+1, end+1)
+	log.Infof("Will retrieve %d records, from %d to %d.", end-from, from+1, end)
 
 	of := cio.NewOutStream(BapiClis.Outfn, "")
 	defer of.Close()
@@ -38,7 +41,7 @@ func Ncbi(BapiClis *types.BapiClisT, ncbiClis *types.NcbiClisT) {
 		bn, n int64
 	)
 	if p.RetMax > end-from {
-		p.RetMax = end - from + 1
+		p.RetMax = end - from
 	}
 	for p.RetStart = from; p.RetStart < end; p.RetStart += p.RetMax {
 		log.Infof("Attempting to retrieve %d records: %d-%d with %d retries.", p.RetMax, p.RetStart+1, p.RetMax+p.RetStart, BapiClis.Retries)

cmd/version.go

@@ -1,3 +1,3 @@
 package cmd
 
-var version = "v0.2.4"
+var version = "v0.2.4-1"

go.mod

@@ -17,7 +17,7 @@ require (
 	github.com/olekukonko/tablewriter v0.0.4
 	github.com/onsi/ginkgo v1.11.0 // indirect
 	github.com/onsi/gomega v1.8.1 // indirect
-	github.com/openbiox/ligo v0.0.0-20200118071238-d342cb716c4e
+	github.com/openbiox/ligo v0.0.0-20200119135627-2571ec0d416e
 	github.com/sirupsen/logrus v1.4.2
 	github.com/spf13/cobra v0.0.5
 	github.com/spf13/pflag v1.0.5 // indirect