/
redcap.go
196 lines (156 loc) · 4.2 KB
/
redcap.go
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package main
import (
"bytes"
"database/sql"
"encoding/csv"
"fmt"
"io/ioutil"
"log"
"regexp"
"strings"
"sync"
_ "github.com/lib/pq"
"github.com/spf13/cobra"
"github.com/spf13/viper"
"github.com/tjrivera/go-cap/redcap"
)
type REDCapConfig struct {
Url string
Projects map[string]string
}
var redcapStagingCmd = &cobra.Command{
Use: "redcap",
Short: "Run Redcap portion of brp_demoETL",
Run: func(cmd *cobra.Command, args []string) {
if len(args) == 0 {
log.Fatal("Error: You must provide a target")
}
staging.Add(1)
redcapStaging(args)
}}
var redcapStaging = func(args []string) {
defer staging.Done()
var Rc REDCapConfig
err := viper.UnmarshalKey("REDCap", &Rc)
if err != nil {
log.Println("unable to decode: %s", err)
}
target := targets[args[0]]
db, err := sql.Open("postgres", fmt.Sprintf("host=%s user=%s dbname=%s sslmode=disable",
target.Host,
target.User,
target.Db))
if err != nil {
log.Fatal(err)
}
defer db.Close()
for _, token := range Rc.Projects {
// Create REDCap project
project := redcap.NewRedcapProject(Rc.Url, token, true)
// Wait group for concurrent form retrieval
var form_retrieval sync.WaitGroup
form_retrieval.Add(len(project.Forms))
// Drop existing tables
for _, form := range project.Forms {
_, err := db.Query(fmt.Sprintf("drop table if exists %s", form.Name))
if err != nil {
log.Fatal(err)
}
}
// Create REDCap base tables
_, err = db.Query(string(project.ToSQL("postgres")))
if err != nil {
log.Fatal("[redcap] error creating base redcap tables. ", err)
}
// Export records for project forms
for _, form := range project.Forms {
// Ignore legacy tables
if !strings.Contains(form.Name, "old") {
// Send concurrent REDCap API request
go func(f *redcap.RedcapForm) {
defer form_retrieval.Done()
params := redcap.ExportParameters{
Fields: []string{project.Unique_key.Field_name, "redcap_event_name"},
Forms: []string{f.Name},
RawOrLabel: "label",
Format: "csv",
ExportCheckboxLabel: true,
}
res := project.ExportRecords(params)
r := bytes.NewReader(res)
// Persist to Postgres
txn, err := db.Begin()
if err != nil {
log.Fatal(err)
}
if err != nil {
log.Fatal("[redcap][database] unable to start transaction", err)
}
reader := csv.NewReader(r)
csvData, err := reader.ReadAll()
if err != nil {
log.Fatal("[redcap] unable to read csv", err)
}
// Prepare INSERT statements from CSV file
for i, line := range csvData {
// skip header line
if i == 0 {
continue
}
for j, value := range line {
// Escape quoted characters and convert to NULL if empty
line[j] = prepareValue(value)
}
values := strings.Join(line, ",")
stmt, err := txn.Prepare(fmt.Sprintf("insert into %s values(%s)", f.Name, values))
if err != nil {
log.Fatal(fmt.Sprintf("[redcap] error formatting insert statement for table %s. ", f.Name), err)
}
if stmt != nil {
_, err = stmt.Exec()
if err != nil {
log.Fatal("[redcap] error executing statement ", err)
}
err = stmt.Close()
}
}
err = txn.Commit()
log.Printf("Loaded REDCap form \"%s\"\n", f.Name)
if err != nil {
log.Fatal("[redcap][database] unable to commit form to table", err)
}
}(form)
} else {
form_retrieval.Done()
}
}
form_retrieval.Wait()
log.Println("REDCap staging completed.")
}
}
var redcapTransform = func(args []string) {
target_config := targets[args[0]]
db, err := sql.Open("postgres", fmt.Sprintf("host=%s user=%s dbname=%s sslmode=disable",
target_config.Host,
target_config.User,
target_config.Db))
if err != nil {
log.Fatal(err)
}
defer db.Close()
stmt, _ := ioutil.ReadFile("transform/REDCapTransform.sql")
_, err = db.Exec(string(stmt))
if err != nil {
log.Fatal(err)
}
log.Println("REDCap transforms complete.")
}
var prepareValue = func(s string) string {
re := regexp.MustCompile("'")
s = re.ReplaceAllString(s, "''")
if s == "" {
return "NULL"
} else {
return fmt.Sprintf("'%s'", s)
}
}