Golang Values.Add方法代码示例

// IsInParentList search an id in the list of parents of the taxon.
func isInParentList(c *cmdapp.Command, db jdh.DB, id string, pIds []string) bool {
	args := new(jdh.Values)
	args.Add(jdh.TaxParents, id)
	pl, err := db.List(jdh.Taxonomy, args)
	if err != nil {
		fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
		os.Exit(1)
	}
	defer pl.Close()
	for {
		p := &jdh.Taxon{}
		if err := pl.Scan(p); err != nil {
			if err == io.EOF {
				break
			}
			fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
			os.Exit(1)
		}
		for _, pid := range pIds {
			if p.Id == pid {
				return true
			}
		}
	}
	return false
}

func getValidParent(c *cmdapp.Command, extId string) string {
	args := new(jdh.Values)
	args.Add(jdh.TaxParents, extId)
	l, err := extDB.List(jdh.Taxonomy, args)
	if err != nil {
		fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
		os.Exit(1)
	}
	defer l.Close()
	for {
		et := &jdh.Taxon{}
		if err := l.Scan(et); err != nil {
			if err == io.EOF {
				break
			}
			fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
			os.Exit(1)
		}
		p := taxon(c, localDB, extDBFlag+":"+et.Id)
		if len(p.Id) > 0 {
			if p.IsValid {
				return p.Id
			} else {
				return p.Parent
			}
		}
	}
	return ""
}

func trForceProc(c *cmdapp.Command, phy *jdh.Phylogeny) {
	txLs := list.New()
	vals := new(jdh.Values)
	vals.Add(jdh.TreTaxon, phy.Id)
	l, err := localDB.List(jdh.Trees, vals)
	if err != nil {
		fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
		os.Exit(1)
	}
	for {
		var tId jdh.IdElement
		if err := l.Scan(&tId); err != nil {
			if err == io.EOF {
				break
			}
			fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
			os.Exit(1)
		}
		if len(tId.Id) == 0 {
			continue
		}
		txLs.PushBack(tId.Id)
	}
	if txLs.Len() == 0 {
		return
	}
	root := phyloNode(c, localDB, phy.Root)
	trForceNode(c, root, txLs)
}

func txEdVal(from *jdh.Taxon) {
	if from.IsValid {
		return
	}
	vals := new(jdh.Values)
	vals.Add(jdh.KeyId, from.Id)
	vals.Add(jdh.TaxValid, "true")
	localDB.Exec(jdh.Set, jdh.Taxonomy, vals)
}

func raLsRun(c *cmdapp.Command, args []string) {
	openLocal(c)
	var tax *jdh.Taxon
	if len(taxonFlag) > 0 {
		tax = taxon(c, localDB, taxonFlag)
		if len(tax.Id) == 0 {
			return
		}
	} else if len(args) > 0 {
		if len(args) > 2 {
			fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("too many arguments"))
			os.Exit(1)
		}
		pName := ""
		if len(args) > 1 {
			pName = args[1]
		}
		tax = pickTaxName(c, localDB, args[0], pName)
		if len(tax.Id) == 0 {
			return
		}
	} else {
		fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("expectiong taxon name or id"))
		c.Usage()
	}
	vals := new(jdh.Values)
	if childFlag {
		vals.Add(jdh.RDisTaxonParent, tax.Id)
	} else {
		vals.Add(jdh.RDisTaxon, tax.Id)
	}
	l := rasList(c, localDB, vals)
	defer l.Close()
	ct := tax
	for {
		ras := &jdh.Raster{}
		if err := l.Scan(ras); err != nil {
			if err == io.EOF {
				break
			}
			fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
			os.Exit(1)
		}
		if machineFlag {
			fmt.Fprintf(os.Stdout, "%s\n", ras.Id)
			continue
		}
		if ras.Taxon != ct.Id {
			ct = taxon(c, localDB, ras.Taxon)
		}
		if verboseFlag {
			fmt.Fprintf(os.Stdout, "%s %s %s\t%s\t%dx%d\n", ct.Id, ct.Name, ct.Authority, ras.Id, ras.Cols, ras.Cols/2)
			continue
		}
		fmt.Fprintf(os.Stdout, "%s\t%s\t%dx%d\n", ct.Name, ras.Id, ras.Cols, ras.Cols/2)
	}
}

func spPopFetch(c *cmdapp.Command, tax *jdh.Taxon, prevRank, rank jdh.Rank) {
	r := tax.Rank
	if r == jdh.Unranked {
		r = prevRank
	}
	defer func() {
		l := getTaxDesc(c, localDB, tax.Id, true)
		spPopNav(c, l, r, rank)
		l = getTaxDesc(c, localDB, tax.Id, false)
		spPopNav(c, l, r, rank)
	}()
	if len(tax.Id) == 0 {
		return
	}
	if r < rank {
		return
	}
	eid := searchExtern(extDBFlag, tax.Extern)
	if len(eid) == 0 {
		return
	}
	vals := new(jdh.Values)
	vals.Add(jdh.SpeTaxon, eid)
	if geoRefFlag {
		vals.Add(jdh.SpeGeoref, "true")
	}
	l := speList(c, extDB, vals)
	for {
		spe := &jdh.Specimen{}
		if err := l.Scan(spe); err != nil {
			if err == io.EOF {
				break
			}
			fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
			os.Exit(1)
		}
		if osp := specimen(c, localDB, extDBFlag+":"+spe.Id); len(osp.Id) > 0 {
			continue
		}
		if len(spe.Catalog) > 0 {
			if osp := specimen(c, localDB, spe.Catalog); len(osp.Id) > 0 {
				exsp := searchExtern(extDBFlag, osp.Extern)
				if exsp == spe.Id {
					continue
				}
				fmt.Fprintf(os.Stderr, "specimen %s already in database as %s [duplicated in %s]\n", spe.Catalog, osp.Id, extDBFlag)
				continue
			}
		}
		addToSpecimens(c, spe, tax.Id)
	}
}

func trDelNode(c *cmdapp.Command) {
	vals := new(jdh.Values)
	if colpFlag {
		vals.Add(jdh.NodCollapse, nodeFlag)
	} else {
		vals.Add(jdh.KeyId, nodeFlag)
	}
	if _, err := localDB.Exec(jdh.Delete, jdh.Nodes, vals); err != nil {
		fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
		os.Exit(1)
	}
	localDB.Exec(jdh.Commit, "", nil)
}

func setNode(nod *jdh.Node, anc *trNode, data *trData) *trNode {
	trn := &trNode{
		id:     nod.Id,
		taxon:  nod.Taxon,
		parent: anc,
	}
	data.node = append(data.node, trn)
	if anc != nil {
		trn.nest = anc.nest + 1
		trn.minX = float32(trn.nest)
	}
	if len(nod.Taxon) > 0 {
		tax := taxon(cmd, localDB, nod.Taxon)
		trn.name.Text = tax.Name
		if !tax.IsValid {
			val := taxon(cmd, localDB, tax.Parent)
			nm := fmt.Sprintf("[%s syn. of %s]", tax.Name, val.Name)
			trn.name.Text = nm
		}
	}
	vals := new(jdh.Values)
	vals.Add(jdh.NodChildren, nod.Id)
	l, err := localDB.List(jdh.Nodes, vals)
	if err != nil {
		fmt.Fprintf(os.Stderr, "%s\n", cmd.ErrStr(err))
		os.Exit(1)
	}
	for {
		desc := &jdh.Node{}
		if err := l.Scan(desc); err != nil {
			if err == io.EOF {
				break
			}
			fmt.Fprintf(os.Stderr, "%s\n", cmd.ErrStr(err))
			os.Exit(1)
		}
		d := setNode(desc, trn, data)
		trn.terms += d.terms
		if trn.level <= d.level {
			trn.level = d.level + 1
		}
		trn.children = append(trn.children, d)
	}
	if len(trn.children) == 0 {
		data.terms++
		trn.terms = 1
	} else {
		sort.Sort(bySize(trn.children))
	}
	return trn
}

// GetTaxDesc return the list of descendants of a taxon.
func getTaxDesc(c *cmdapp.Command, db jdh.DB, id string, valid bool) jdh.ListScanner {
	args := new(jdh.Values)
	if valid {
		args.Add(jdh.TaxChildren, id)
	} else {
		args.Add(jdh.TaxSynonyms, id)
	}
	l, err := db.List(jdh.Taxonomy, args)
	if err != nil {
		fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
		os.Exit(1)
	}
	return l
}

func dsDelRun(c *cmdapp.Command, args []string) {
	if len(idFlag) == 0 {
		fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("expectiong dataset id"))
		c.Usage()
	}
	openLocal(c)
	vals := new(jdh.Values)
	vals.Add(jdh.KeyId, idFlag)
	if _, err := localDB.Exec(jdh.Delete, jdh.Datasets, vals); err != nil {
		fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
		os.Exit(1)
	}
	localDB.Exec(jdh.Commit, "", nil)
}

func txEdSyn(from, to *jdh.Taxon) {
	if from.Id == "0" {
		return
	}
	if from.Id == to.Id {
		return
	}
	if (from.Parent == to.Id) && (!from.IsValid) {
		return
	}
	vals := new(jdh.Values)
	vals.Add(jdh.KeyId, from.Id)
	vals.Add(jdh.TaxSynonym, to.Id)
	localDB.Exec(jdh.Set, jdh.Taxonomy, vals)
}

func trForceNode(c *cmdapp.Command, nod *jdh.Node, txLs *list.List) {
	vals := new(jdh.Values)
	vals.Add(jdh.NodChildren, nod.Id)
	l, err := localDB.List(jdh.Nodes, vals)
	if err != nil {
		fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
		os.Exit(1)
	}
	childs := 0
	for {
		desc := &jdh.Node{}
		if err := l.Scan(desc); err != nil {
			if err == io.EOF {
				break
			}
			fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
			os.Exit(1)
		}
		trForceNode(c, desc, txLs)
		childs++
	}
	if childs > 1 {
		return
	}
	if len(nod.Taxon) == 0 {
		return
	}
	tax := taxon(c, localDB, nod.Taxon)
	if tax.IsValid {
		return
	}
	par := taxon(c, localDB, tax.Parent)
	todel := false
	for e := txLs.Front(); e != nil; e = e.Next() {
		tId := e.Value.(string)
		if tId == par.Id {
			todel = true
			break
		}
	}
	if todel {
		fmt.Fprintf(os.Stdout, "%s: deleted\n", tax.Name)
		if !repFlag {
			vals.Reset()
			vals.Add(jdh.KeyId, nod.Id)
			localDB.Exec(jdh.Delete, jdh.Nodes, vals)
		}
		return
	}
	fmt.Fprintf(os.Stdout, "%s: changed to: %s\n", tax.Name, par.Name)
	if !repFlag {
		vals.Reset()
		vals.Add(jdh.KeyId, nod.Id)
		vals.Add(jdh.NodTaxon, par.Id)
		localDB.Exec(jdh.Set, jdh.Nodes, vals)
		txLs.PushBack(par.Id)
	}
}

func newTxList(tax *jdh.Taxon, db jdh.DB, syns bool) *txList {
	ls := &txList{
		db:   db,
		tax:  tax,
		syns: syns,
	}
	id := ""
	if tax == nil {
		ls.tax = &jdh.Taxon{
			Id:   "0",
			Name: "root",
		}
	} else {
		id = tax.Id
	}
	vals := new(jdh.Values)
	vals.Add(jdh.TaxChildren, id)
	pl, err := db.List(jdh.Taxonomy, vals)
	if err != nil {
		return ls
	}
	for {
		d := &jdh.Taxon{}
		if err := pl.Scan(d); err != nil {
			break
		}
		ls.desc = append(ls.desc, d)
	}
	if !syns {
		return ls
	}
	vals.Reset()
	vals.Add(jdh.TaxSynonyms, id)
	pl, err = db.List(jdh.Taxonomy, vals)
	if err != nil {
		return ls
	}
	for {
		s := &jdh.Taxon{}
		if err := pl.Scan(s); err != nil {
			break
		}
		ls.desc = append(ls.desc, s)
	}
	return ls
}

func trDelRun(c *cmdapp.Command, args []string) {
	openLocal(c)
	if len(nodeFlag) > 0 {
		trDelNode(c)
		return
	}
	if len(idFlag) == 0 {
		fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("expectiong tree or node id"))
		c.Usage()
	}
	vals := new(jdh.Values)
	vals.Add(jdh.KeyId, idFlag)
	if _, err := localDB.Exec(jdh.Delete, jdh.Trees, vals); err != nil {
		fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
		os.Exit(1)
	}
	localDB.Exec(jdh.Commit, "", nil)
}

func trLsNodes(c *cmdapp.Command) {
	vals := new(jdh.Values)
	if ancsFlag {
		vals.Add(jdh.NodParent, nodeFlag)
	} else {
		vals.Add(jdh.NodChildren, nodeFlag)
	}
	l, err := localDB.List(jdh.Nodes, vals)
	if err != nil {
		fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
		os.Exit(1)
	}
	for {
		nod := &jdh.Node{}
		if err := l.Scan(nod); err != nil {
			if err == io.EOF {
				break
			}
			fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
			os.Exit(1)
		}
		if machineFlag {
			fmt.Fprintf(os.Stdout, "%s\n", nod.Id)
			continue
		}
		var tax *jdh.Taxon
		if len(nod.Taxon) > 0 {
			tax = taxon(c, localDB, nod.Taxon)
		}
		if verboseFlag {
			fmt.Fprintf(os.Stdout, "%s\t", nod.Id)
			if tax != nil {
				fmt.Fprintf(os.Stdout, "%s [id:%s]", tax.Name, tax.Id)
			}
			fmt.Fprintf(os.Stdout, "\tlen: %d\tage: %d\n", nod.Len, nod.Age)
			continue
		}
		fmt.Fprintf(os.Stdout, "%s\t", nod.Id)
		if tax != nil {
			fmt.Fprintf(os.Stdout, "%s", tax.Name)
		}
		fmt.Fprintf(os.Stdout, "\n")
	}
}