Data input class

Represents a single input data file with its ID and path. This is a minimal representation that will be extended later with reading/writing capabilities.

Public fields

id

Character. The canonical identifier for this input (e.g., "feature_table")

path

Character. The absolute path to the input file

Methods

Public methods

• PMData$new()

• PMData$print()

• PMData$read()

• PMData$exists()

• PMData$write()

• PMData$clone()

---

Method new()

Create a PMData object

Usage

PMData$new(id, path)

Arguments

id

Character. The canonical identifier for this input

path

Character. The absolute path to the input file

---

Method print()

Print method for PMData

Usage

PMData$print()

---

Method read()

Read the data file

Usage

PMData$read(...)

Arguments

...

Additional arguments passed to pm_read_file

Returns

The contents of the file. For RData files, returns a new environment containing all objects from the file.

Examples

\dontrun{
data <- PMData$new(id = "feature_table", path = "/path/to/file.csv")
contents <- data$read()
}

---

Method exists()

Check if the data file exists

Usage

PMData$exists()

Returns

Logical. TRUE if the file exists, FALSE otherwise.

Examples

withr::with_tempdir({
  data <- PMData$new(id = "feature_table", path = "file.csv")
  data$exists()  # FALSE - file doesn't exist yet

  df <- data.frame(x = 1:5, y = letters[1:5])
  data$write(df)
  data$exists()  # TRUE - file now exists
})

---

Method write()

Write data to the file

Usage

PMData$write(x, ...)

Arguments

x

The object to write. For tabular formats (CSV, TSV, Parquet), must be a data.frame. For RData files, can accept multiple objects via ....

...

Additional arguments passed to pm_write_file. For RData files, additional objects can be provided here.

Returns

Invisibly returns the file path.

Examples

withr::with_tempdir({
  data <- PMData$new(id = "feature_table", path = "file.csv")
  df <- data.frame(x = 1:5, y = letters[1:5])
  data$write(df)

  # For RData files, can write multiple objects
  data_rdata <- PMData$new(id = "results", path = "results.RData")
  obj1 <- data.frame(x = 1:3)
  obj2 <- c("a", "b", "c")
  data_rdata$write(obj1, obj2, obj3 = 42)
})

---

Method clone()

The objects of this class are cloneable with this method.

Usage

PMData$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

data <- PMData$new(id = "feature_table", path = "/path/to/file.biom")
data$id
#> [1] "feature_table"
data$path
#> [1] "/path/to/file.biom"


## ------------------------------------------------
## Method `PMData$read`
## ------------------------------------------------

if (FALSE) { # \dontrun{
data <- PMData$new(id = "feature_table", path = "/path/to/file.csv")
contents <- data$read()
} # }

## ------------------------------------------------
## Method `PMData$exists`
## ------------------------------------------------

withr::with_tempdir({
  data <- PMData$new(id = "feature_table", path = "file.csv")
  data$exists()  # FALSE - file doesn't exist yet

  df <- data.frame(x = 1:5, y = letters[1:5])
  data$write(df)
  data$exists()  # TRUE - file now exists
})
#> [1] TRUE

## ------------------------------------------------
## Method `PMData$write`
## ------------------------------------------------

withr::with_tempdir({
  data <- PMData$new(id = "feature_table", path = "file.csv")
  df <- data.frame(x = 1:5, y = letters[1:5])
  data$write(df)

  # For RData files, can write multiple objects
  data_rdata <- PMData$new(id = "results", path = "results.RData")
  obj1 <- data.frame(x = 1:3)
  obj2 <- c("a", "b", "c")
  data_rdata$write(obj1, obj2, obj3 = 42)
})