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textToDb.go
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textToDb.go
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// Copyright (c) 2016 OpenM++
// This code is licensed under the MIT license (see LICENSE.txt for details)
package main
import (
"database/sql"
"encoding/csv"
"errors"
"io"
"os"
"path/filepath"
"strings"
"github.com/openmpp/go/ompp/config"
"github.com/openmpp/go/ompp/db"
"github.com/openmpp/go/ompp/helper"
"github.com/openmpp/go/ompp/omppLog"
)
// copy model from text json and csv files into database
func textToDb(modelName string, runOpts *config.RunOptions) error {
// validate parameters
if modelName == "" {
return errors.New("invalid (empty) model name")
}
// open source database connection and check is it valid
dn := runOpts.String(toDbDriverArgKey)
if dn == "" && runOpts.IsExist(dbDriverArgKey) {
dn = runOpts.String(dbDriverArgKey)
}
cs, dn := db.IfEmptyMakeDefault(modelName, runOpts.String(toSqliteArgKey), runOpts.String(toDbConnStrArgKey), dn)
dstDb, dbFacet, err := db.Open(cs, dn, true)
if err != nil {
return err
}
defer dstDb.Close()
if err := db.CheckOpenmppSchemaVersion(dstDb); err != nil {
return err
}
// use modelName as subdirectory inside of input and output directories or as name of model.zip file
inpDir := runOpts.String(inputDirArgKey)
if !runOpts.Bool(zipArgKey) {
inpDir = filepath.Join(inpDir, modelName) // json and csv files located in modelName subdir
} else {
omppLog.Log("Unpack ", modelName, ".zip")
outDir := runOpts.String(outputDirArgKey)
if outDir == "" {
outDir = filepath.Dir(inpDir)
}
if err = helper.UnpackZip(filepath.Join(inpDir, modelName+".zip"), outDir); err != nil {
return err
}
inpDir = filepath.Join(outDir, modelName)
}
// insert model metadata from json file into database
modelDef, err := fromModelJsonToDb(dstDb, dbFacet, inpDir, modelName)
if err != nil {
return err
}
// insert languages and model text metadata from json file into database
langDef, err := fromLangTextJsonToDb(dstDb, modelDef, inpDir)
if err != nil {
return err
}
// insert model runs data from csv into database:
// parameters, output expressions and accumulators
dblFmt := runOpts.String(doubleFormatArgKey)
encName := runOpts.String(encodingArgKey)
isNoModelDigestCheck := runOpts.Bool(noDigestCheck)
if err = fromRunTextListToDb(dstDb, modelDef, langDef, inpDir, isNoModelDigestCheck, dblFmt, encName); err != nil {
return err
}
// insert model workset data from csv into database: input parameters
if err = fromWorksetTextListToDb(dstDb, modelDef, langDef, inpDir, isNoModelDigestCheck, dblFmt, encName); err != nil {
return err
}
// insert modeling tasks and tasks run history from json file into database
if err = fromTaskListJsonToDb(dstDb, modelDef, langDef, inpDir); err != nil {
return err
}
return nil
}
// fromModelJsonToDb reads model metadata from json file and insert it into database.
func fromModelJsonToDb(dbConn *sql.DB, dbFacet db.Facet, inpDir string, modelName string) (*db.ModelMeta, error) {
// restore model metadta from json
js, err := helper.FileToUtf8(filepath.Join(inpDir, modelName+".model.json"), "")
if err != nil {
return nil, err
}
modelDef := &db.ModelMeta{}
isExist, err := modelDef.FromJson([]byte(js))
if err != nil {
return nil, err
}
if !isExist {
return nil, errors.New("model not found: " + modelName)
}
if modelDef.Model.Name != modelName {
return nil, errors.New("model name: " + modelName + " not found in .json file")
}
// insert model metadata into destination database if not exists
if _, err = db.UpdateModel(dbConn, dbFacet, modelDef); err != nil {
return nil, err
}
// insert, update or delete model default profile
var modelProfile db.ProfileMeta
isExist, err = helper.FromJsonFile(filepath.Join(inpDir, modelName+".profile.json"), &modelProfile)
if err != nil {
return nil, err
}
if isExist && modelProfile.Name == modelName { // if this is profile default model profile then do update
if err = db.UpdateProfile(dbConn, &modelProfile); err != nil {
return nil, err
}
}
return modelDef, nil
}
// fromLangTextJsonToDb reads languages and model text from json file and insert it into database.
func fromLangTextJsonToDb(dbConn *sql.DB, modelDef *db.ModelMeta, inpDir string) (*db.LangMeta, error) {
// restore language list from json and if exist then update db tables
js, err := helper.FileToUtf8(filepath.Join(inpDir, modelDef.Model.Name+".lang.json"), "")
if err != nil {
return nil, err
}
langDef := &db.LangMeta{}
isExist, err := langDef.FromJson([]byte(js))
if err != nil {
return nil, err
}
if isExist {
if err = db.UpdateLanguage(dbConn, langDef); err != nil {
return nil, err
}
}
// get full list of languages
langDef, err = db.GetLanguages(dbConn)
if err != nil {
return nil, err
}
// restore text data from json and if exist then update db tables
var modelTxt db.ModelTxtMeta
isExist, err = helper.FromJsonFile(filepath.Join(inpDir, modelDef.Model.Name+".text.json"), &modelTxt)
if err != nil {
return nil, err
}
if isExist {
if err = db.UpdateModelText(dbConn, modelDef, langDef, &modelTxt); err != nil {
return nil, err
}
}
// restore model language-specific strings from json and if exist then update db table
var mwDef db.ModelWordMeta
isExist, err = helper.FromJsonFile(filepath.Join(inpDir, modelDef.Model.Name+".word.json"), &mwDef)
if err != nil {
return nil, err
}
if isExist {
if err = db.UpdateModelWord(dbConn, modelDef, langDef, &mwDef); err != nil {
return nil, err
}
}
return langDef, nil
}
// fromTableCsvFile read output table csv files (accumulators and expressions) and write it into db output tables.
func fromTableCsvFile(
dbConn *sql.DB,
modelDef *db.ModelMeta,
layout db.WriteTableLayout,
csvDir string,
cvtExpr db.CellExprConverter,
cvtAcc db.CellAccConverter,
encodingName string) error {
// accumulator converter from csv row []string to db cell
aToCell, err := cvtAcc.CsvToCell(modelDef, layout.Name, layout.SubCount)
if err != nil {
return errors.New("invalid converter from accumulators csv row: " + err.Error())
}
// open accumulators csv file
aFn, err := cvtAcc.CsvFileName(modelDef, layout.Name, false)
if err != nil {
return errors.New("invalid accumulators csv file name: " + err.Error())
}
ahs, err := cvtAcc.CsvHeader(modelDef, layout.Name)
if err != nil {
return errors.New("Error at building csv accumulators header " + layout.Name + ": " + err.Error())
}
ah := strings.Join(ahs, ",")
accFile, err := os.Open(filepath.Join(csvDir, aFn))
if err != nil {
return errors.New("accumulators csv file open error: " + err.Error())
}
defer accFile.Close()
accFrom, err := makeFromCsvReader(aFn, accFile, encodingName, ah, aToCell)
if err != nil {
return errors.New("fail to create expressions csv reader: " + err.Error())
}
// expression converter from csv row []string to db cell
eToCell, err := cvtExpr.CsvToCell(modelDef, layout.Name, layout.SubCount)
if err != nil {
return errors.New("invalid converter from expressions csv row: " + err.Error())
}
// open expressions csv file
eFn, err := cvtExpr.CsvFileName(modelDef, layout.Name, false)
if err != nil {
return errors.New("invalid expressions csv file name: " + err.Error())
}
ehs, err := cvtExpr.CsvHeader(modelDef, layout.Name)
if err != nil {
return errors.New("Error at building csv expressions header " + layout.Name + ": " + err.Error())
}
eh := strings.Join(ehs, ",")
exprFile, err := os.Open(filepath.Join(csvDir, eFn))
if err != nil {
return errors.New("expressions csv file open error: " + err.Error())
}
defer exprFile.Close()
exprFrom, err := makeFromCsvReader(eFn, exprFile, encodingName, eh, eToCell)
if err != nil {
return errors.New("fail to create expressions csv reader: " + err.Error())
}
// write each accumulator(s) csv rows into accumulator(s) output table
// write each expression(s) csv rows into expression(s) output table
err = db.WriteOutputTableFrom(dbConn, modelDef, &layout, accFrom, exprFrom)
if err != nil {
return err
}
return nil
}
// return closure to iterate over csv file rows
func makeFromCsvReader(
fileName string, csvFile *os.File, encodingName string, csvHeader string, csvToCell func(row []string) (interface{}, error),
) (func() (interface{}, error), error) {
// create csv reader from utf-8 line
uRd, err := helper.Utf8Reader(csvFile, encodingName)
if err != nil {
return nil, errors.New("fail to create utf-8 converter: " + err.Error())
}
csvRd := csv.NewReader(uRd)
csvRd.TrimLeadingSpace = true
csvRd.ReuseRecord = true
// skip header line
fhs, e := csvRd.Read()
switch {
case e == io.EOF:
return nil, errors.New("invalid (empty) csv file: " + fileName)
case err != nil:
return nil, errors.New("csv file read error: " + fileName + ": " + err.Error())
}
fh := strings.Join(fhs, ",")
if strings.HasPrefix(fh, string(helper.Utf8bom)) {
fh = fh[len(helper.Utf8bom):]
}
if fh != csvHeader {
return nil, errors.New("Invalid csv file header " + fileName + ": " + fh + " expected: " + csvHeader)
}
// convert each csv line into cell (id cell)
// reading from .id.csv files not supported by converters
from := func() (interface{}, error) {
row, err := csvRd.Read()
switch {
case err == io.EOF:
return nil, nil // eof
case err != nil:
return nil, errors.New("csv file read error: " + fileName + ": " + err.Error())
}
// convert csv line to cell and return from reader
c, err := csvToCell(row)
if err != nil {
return nil, errors.New("csv file row convert error: " + fileName + ": " + err.Error())
}
return c, nil
}
return from, nil
}