# Analysing phenotype microarray data: database I/O with `RODBC`
This is example R code for using **opm** to store PM data in a database
accessible via `ODBC` and retrieving them again.

This code can be used to check whether a database either found in an
environment variable or identical to the default value (see below) is
correctly set up for this purpose. The code also shows how to include a
user-defined selection of metadata.

**Note**: The `ODBC` connection must be accordingly defined beforehand to
allow for the simple-minded connection attempt stated below. The database
tables must have been set up using the `SQL` that comes with **opm**.

Author: *Markus Goeker*

```{r }
library(opm)
library(opmextra)
library(RODBC)
```

This tries to get the `DSN` from the R or environment variable `RODBC_DSN`:

```{r }
if (exists("RODBC_DSN")) {
  dsn <- RODBC_DSN
} else {
  dsn <- Sys.getenv("RODBC_DSN", "test_opm")
}

print(dsn)
conn <- odbcConnect(dsn)
```

Insertions via **RODBC** in this manner are slow. Creating subsets speeds
things up.


```{r }
result <- opm_dbcheck(conn, time.points = 1:5, wells = 12:14)
```

### Check without metadata

```{r }
print(opm_dbnext(2L, conn))
```

### Check with metadata

```{r }
if (all(result == "ok")) {

  # addition of metadata columns
  sqlQuery(conn,
    "ALTER TABLE plates ADD COLUMN strain text, ADD COLUMN replicate integer;")

  # check with metadata
  md <- data.frame(strain = c("X", "Y"), replicate = c(3L, 7L),
    stringsAsFactors = FALSE)
  result2 <- opm_dbcheck(conn, md, time.points = 1:5, wells = 12:14)

  # removal of metadata columns
  sqlQuery(conn,
    "ALTER TABLE plates DROP COLUMN strain, DROP COLUMN replicate;")

}
```

### Tidying up

```{r }
odbcClose(conn)
rm(conn)

print(result)
stopifnot(result == "ok")
print(result2)
stopifnot(result2 == "ok")


detach("package:opmextra")
detach("package:RODBC")
```

