Golang cmdapp.Command类代码示例

// TaxInDB returns true if a taxon is in the database.
func taxInDB(c *cmdapp.Command, db jdh.DB, name, parent string, rank jdh.Rank, valid bool) *jdh.Taxon {
	args := new(jdh.Values)
	args.Add(jdh.TaxName, name)
	if len(parent) != 0 {
		args.Add(jdh.TaxParent, parent)
	}
	if rank != jdh.Unranked {
		args.Add(jdh.TaxRank, rank.String())
	}
	l, err := db.List(jdh.Taxonomy, args)
	if err != nil {
		fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
		os.Exit(1)
	}
	defer l.Close()
	for {
		tax := &jdh.Taxon{}
		if err := l.Scan(tax); err != nil {
			if err == io.EOF {
				return nil
			}
		}
		if len(tax.Id) > 0 {
			if tax.IsValid == valid {
				return tax
			}
		}
	}
}

func trForceRun(c *cmdapp.Command, args []string) {
	openLocal(c)
	if len(idFlag) > 0 {
		phy := phylogeny(c, localDB, idFlag)
		if len(phy.Id) == 0 {
			return
		}
		trForceProc(c, phy)
		localDB.Exec(jdh.Commit, "", nil)
		return
	}
	l, err := localDB.List(jdh.Trees, new(jdh.Values))
	if err != nil {
		fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
		os.Exit(1)
	}
	for {
		phy := &jdh.Phylogeny{}
		if err := l.Scan(phy); err != nil {
			if err == io.EOF {
				break
			}
			fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
			os.Exit(1)
		}
		if len(phy.Id) == 0 {
			continue
		}
		trForceProc(c, phy)
	}
	localDB.Exec(jdh.Commit, "", nil)
}

func txSetRun(c *cmdapp.Command, args []string) {
	openLocal(c)
	var tax *jdh.Taxon
	if len(idFlag) > 0 {
		tax = taxon(c, localDB, idFlag)
		if len(tax.Id) == 0 {
			return
		}
	} else if (len(args) > 0) && (strings.Index(args[0], "=") < 0) {
		name := args[0]
		pName := ""
		args = args[1:]
		if (len(args) > 0) && (strings.Index(args[0], "=") < 0) {
			pName = args[0]
			args = args[1:]

		}
		tax = pickTaxName(c, localDB, name, pName)
		if len(tax.Id) == 0 {
			return
		}
	} else {
		fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("expectiong taxon name or id"))
		c.Usage()
	}
	vals := valsFromArgs(tax.Id, args)
	localDB.Exec(jdh.Set, jdh.Taxonomy, vals)
	localDB.Exec(jdh.Commit, "", nil)
}

func trLsRun(c *cmdapp.Command, args []string) {
	openLocal(c)
	if len(nodeFlag) > 0 {
		trLsNodes(c)
		return
	}
	l, err := localDB.List(jdh.Trees, new(jdh.Values))
	if err != nil {
		fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
		os.Exit(1)
	}
	for {
		phy := &jdh.Phylogeny{}
		if err := l.Scan(phy); 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", phy.Id)
			continue
		}
		if verboseFlag {
			fmt.Fprintf(os.Stdout, "%s\t%s\troot: %s\n", phy.Id, phy.Name, phy.Root)
			continue
		}
		fmt.Fprintf(os.Stdout, "%s\troot: %s\n", phy.Name, phy.Root)
	}
}

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 txSyncPopDesc(c *cmdapp.Command, l jdh.ListScanner, p *jdh.Taxon) {
	pId := p.Id
	if !p.IsValid {
		pId = p.Parent
	}
	for {
		desc := &jdh.Taxon{}
		if err := l.Scan(desc); err != nil {
			if err == io.EOF {
				break
			}
			fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
			os.Exit(1)
		}
		// check if the taxon is in the database
		if d := taxon(c, localDB, extDBFlag+":"+desc.Id); len(d.Id) != 0 {
			continue
		}
		// adds the new taxon
		tax := &jdh.Taxon{}
		*tax = *desc
		tax.Id = ""
		tax.Parent = pId
		tax.Extern = []string{extDBFlag + ":" + desc.Id}
		if _, err := localDB.Exec(jdh.Add, jdh.Taxonomy, tax); err != nil {
			fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
			os.Exit(1)
		}
	}
}

func dsInRun(c *cmdapp.Command, args []string) {
	openLocal(c)
	format := "txt"
	if len(formatFlag) > 0 {
		format = formatFlag
	}
	if len(args) > 0 {
		switch format {
		case "txt":
			for _, fname := range args {
				dsInTxt(c, fname)
			}
		default:
			fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("format "+format+" unknown"))
			os.Exit(1)
		}
	} else {
		switch format {
		case "txt":
			dsInTxt(c, "")
		default:
			fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr("format "+format+" unknown"))
			os.Exit(1)
		}
	}
	localDB.Exec(jdh.Commit, "", nil)
}

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 ""
}

// 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 dsInTxt(c *cmdapp.Command, fname string) {
	var in *bufio.Reader
	if len(fname) > 0 {
		f, err := os.Open(fname)
		if err != nil {
			fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
			return
		}
		defer f.Close()
		in = bufio.NewReader(f)
	} else {
		in = bufio.NewReader(os.Stdin)
	}
	for {
		tn, err := readLine(in)
		if err != nil {
			break
		}
		ln := strings.Join(tn, " ")
		set := &jdh.Dataset{
			Title: ln,
		}
		id, err := localDB.Exec(jdh.Add, jdh.Datasets, set)
		if err != nil {
			fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
			continue
		}
		if verboseFlag {
			fmt.Fprintf(os.Stdout, "%s %s\n", id, set.Title)
		}
	}
}

// RasList returns a raster distribution list scanner.
func rasList(c *cmdapp.Command, db jdh.DB, vals *jdh.Values) jdh.ListScanner {
	l, err := localDB.List(jdh.RasDistros, vals)
	if err != nil {
		fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
		os.Exit(1)
	}
	return l
}

// openDB opens a database.
func openDB(c *cmdapp.Command, driver, par string) jdh.DB {
	db, err := jdh.Open(driver, par)
	if err != nil {
		fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
		os.Exit(1)
	}
	return db
}

// SpeList returns an specimen list scanner.
func speList(c *cmdapp.Command, db jdh.DB, vals *jdh.Values) jdh.ListScanner {
	l, err := db.List(jdh.Specimens, vals)
	if err != nil {
		fmt.Fprintf(os.Stderr, "%s\n", c.ErrStr(err))
		os.Exit(1)
	}
	return l
}

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 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)
	}
}