Package 'repo'

Description

Repo: The Data-centered Data Flow Manager

Details

The Repo package is meant to help with the management of R data files. It builds one (or more) centralized repository where R objects are stored together with corresponding annotations, tags, dependency notes, provenance traces. It also provides navigation tools to easily locate and load previously stored resources.

Create a new repository with rp <- repo_open().

Given the object rp of class repo, the repo command foo must be called like this: rp$foo(). However, the public name of foo will be repo_foo, and this name must be used to get help (?repo_foo).

For a complete list of functions, use library(help = "repo").

Author(s)

Francesco Napolitano [email protected]

Description

Create a new item from an existing file.

Usage

repo_attach(
  filepath,
  description = NULL,
  tags = NULL,
  prj = NULL,
  src = NULL,
  chunk = basename(filepath),
  replace = F,
  to = NULL,
  URL = NULL
)

Arguments

Value

Used for side effects.

Examples

rp_path <- file.path(tempdir(), "example_repo")
rp <- repo_open(rp_path, TRUE)

## Not run: 
## Creating a PDF file with a figure.
pdf("afigure.pdf")
## Drawing a random plot in the figure
plot(runif(100), runif(100))
dev.off()
## Attaching the PDF file to the repo
rp$attach("afigure.pdf", "A plot of random numbers", "repo_sys")
## don't need the PDF file anymore
file.remove("afigure.pdf")
## Opening the stored PDF with Evince document viewer
rp$sys("afigure.pdf", "evince")

## End(Not run)

## wiping temporary repo
unlink(rp_path, TRUE)

Description

Get item attribute.

Usage

repo_attr(name, attrib)

Arguments

Value

The item's attribute value.

See Also

repo_entries, repo_get

Examples

rp_path <- file.path(tempdir(), "example_repo")
rp <- repo_open(rp_path, TRUE)
rp$put(1, "item1", "Sample item 1", "tag1")
print(rp$attr("item1", "path"))

## wiping temporary repo
unlink(rp_path, TRUE)

Description

In order to be buildable, a repository item must have an associated source file and code chunk.

Usage

repo_build(
  name,
  src = NULL,
  recursive = T,
  force = F,
  env = parent.frame(),
  built = list()
)

Arguments

Details

Code chunks are defined as in the following example: “' ## chunk "item 1" x <- code_to_make_x() rp$put(x, "item 1") ## “'

'item 1' must be associated to the source ('src' parameter of 'put') containing the chunk code.

Value

Nothing, used for side effects.

Description

Edit all items info using a text file.

Usage

repo_bulkedit(outfile = NULL, infile = NULL)

Arguments

Details

Exactly one of outfile or infile must be supplied. All repository entry fields are copied to a tab-separated file when using the outfile parameter. All repo entries are updated reading from infile when the infile parameter is used. Within the TAGS field, tags must be comma-separated. The system writes a checksum to the outfile that prevents from using it as infile if repo has changed in the meantime.

Value

Used for side effects.

See Also

repo_set

Examples

rp_path <- file.path(tempdir(), "example_repo")
rp <- repo_open(rp_path, TRUE)
rp$put(1, "item1", "Sample item 1", c("tag1", "tag2"))

items_data_file <- tempfile()
rp$bulkedit(items_data_file)
## Manually edit items_data_file, then update items:
rp$bulkedit(infile=items_data_file)

## wiping temporary repo
unlink(rp_path, TRUE)

Description

Checks that all indexed data are present in the repository root, that files are not corrupt and that no unindexed files are present.

Usage

repo_check()

Details

Every time the object associated to an item is stored, an MD5 checksum is saved to the repository index. check will use those to verify that the object was not changed by anything other than Repo itself.

Value

Used for side effects.

Examples

## Repository creation
rp_path <- file.path(tempdir(), "example_repo")
rp <- repo_open(rp_path, TRUE)

rp_path <- file.path(tempdir(), "example_repo")
rp <- repo_open(rp_path, TRUE)
rp$put(0, "item1", "A sample item", "repo_check")
rp$check()

## wiping temporary repo
unlink(rp_path, TRUE)

Description

Shows code chunk associated with an item

Usage

repo_chunk(name)

Arguments

Value

List of lines of code, invisibly.

Description

Copies an object file from one repository to another and creates a new entry in the index of the destination repository. Supports tags and multiple names.

Usage

repo_copy(destrepo, name, tags = NULL, replace = F, confirm = T)

Arguments

Value

Used for side effects.

Examples

## Repository creation
rp_path1 <- file.path(tempdir(), "example_repo1")

rp1 <- repo_open(rp_path1, TRUE)
rp1$put(0, "item1", "A sample item", "tag1")
rp_path2 <- file.path(tempdir(), "example_repo2")
rp2 <- repo_open(rp_path2, TRUE)
rp1$copy(rp2, "item1")

## wiping temporary repo
unlink(rp_path1, TRUE)
unlink(rp_path2, TRUE)

Description

Opens a browser window with a Shiny interface to a repo. The interface is preliminary and has some exploration features together with a "Load into workspace" button for a selected item.

Usage

repo_cpanel(reporoot = NULL, env = globalenv())

Arguments

Value

Used for side effects.

Description

Creates a weighted adjacency matrix, in which (i,j) = x means that item i is in relation x with item j. The resulting graph is plotted.

Usage

repo_dependencies(
  tags = NULL,
  tagfun = "OR",
  depends = T,
  attached = T,
  generated = T,
  plot = T,
  ...
)

Arguments

Details

The relation between any two items i and j can have values 1, 2 or 3, respectively meaning:

• depends on: to build item i, item j was necessary.

• attached to: item i is an attachment item and is attached to item j.

• generated by: item i has been generated by item j. Item j is usually an attachment containing the source code that generated item i.

Value

Adjacency matrix representing the graph, with edges labeled 1, 2, 3 corresponding to "depends", "attached" and "generated" respectively.

Examples

## Repository creation
rp_path <- file.path(tempdir(), "example_repo")
rp <- repo_open(rp_path, TRUE)

## Producing some irrelevant data
data1 <- 1:10
data2 <- data1 * 2
data3 <- data1 + data2

## Putting the data in the database, specifying dependencies
rp$put(data1, "item1", "First item",
    "repo_dependencies")
rp$put(data2, "item2", "Item dependent on item1", 
    "repo_dependencies", depends="item1")
rp$put(data3, "item3", "Item dependent on item1 and item2",
    "repo_dependencies", depends=c("item1", "item2"))

## Creating a temporary plot and attaching it
fpath <- file.path(rp$root(), "temp.pdf")
pdf(fpath)
plot(data1)
dev.off()
rp$attach(fpath, "visualization of item1", "plot",
   to="item1")

## Obtaining the dependency matrix
depmat <- rp$dependencies(plot=FALSE)
print(depmat)
## The matrix can be plotted as a graph (requires igraph package)
rp$dependencies()
## The following hides "generated" edges
rp$dependencies(generated=FALSE)

## wiping temporary repo
unlink(rp_path, TRUE)

Description

Returns item's dependencies

Usage

repo_depends(name)

Arguments

Value

The items on which the input item depends.

Description

Low-level list of item entries.

Usage

repo_entries()

Value

A detailed list of item entries.

Examples

rp_path <- file.path(tempdir(), "example_repo")
rp <- repo_open(rp_path, TRUE)
rp$put(1, "item1", "Sample item 1", "entries")
rp$put(2, "item2", "Sample item 2", "entries")
rp$put(3, "item3", "Sample item 3", "entries")
print(rp$entries())

## wiping temporary repo
unlink(rp_path, TRUE)

Description

Export repo items to RDS file.

Usage

repo_export(name, where = ".", tags = NULL, askconfirm = T)

Arguments

Value

TRUE on success, FALSE otherwise.

Examples

rp_path <- file.path(tempdir(), "example_repo")
rp <- repo_open(rp_path, TRUE)
rp$put(1, "item1", "Sample item 1", "export")
rp$export("item1", tempdir()) # creates item1.RDS in a tempdir

## wiping temporary repo
unlink(rp_path, TRUE)

Description

Match items by matching any field

Usage

repo_find(what, all = F, show = "ds")

Arguments

Details

This function actually calls print specifying the find parameters. The find parameter can be any character string to be matched against any item field, including string-converted size (like "10x3").

Value

Used for side effects.

Examples

rp_path <- file.path(tempdir(), "example_repo")

rp <- repo_open(rp_path, TRUE)
rp$put(1, "item1", "Sample item 1", c("tag1", "tag2"))
rp$put(2, "item2", "Sample item 2", c("tag1", "hide"))
rp$put(3, "item3", "Sample item 3", c("tag2", "tag3"))
rp$print()
rp$find("tEm2")
rp$find("ag2", show="t")

## wiping the temp repo
unlink(rp_path, TRUE)

Description

Retrieve an item from the repo.

Usage

repo_get(name, enableSuggestions = T)

Arguments

Value

The previously stored object, or its file system path for attachments.

Examples

rp_path <- file.path(tempdir(), "example_repo")
rp <- repo_open(rp_path, TRUE)
rp$put(1, "item1", "Sample item 1", "get")
print(rp$get("item1"))

## wiping temporary repo
unlink(rp_path, TRUE)

Description

Creates a list of functions, each one associated with a repository item, that can be used to access items directly.

Usage

repo_handlers()

Details

Repository handlers are functions associated with items. As opposed to item names, they can take advantage of IDE auto-completion features and do not require quotation marks. A handler to the repo object itself is provided in the list.

Value

A list of functions.

Examples

## Repository creation
rp_path <- file.path(tempdir(), "example_repo")
rp <- repo_open(rp_path, TRUE)

## Putting some irrelevant data
rp$put(1, "item1", "Sample item 1", "repo_handlers")
rp$put(2, "item2", "Sample item 2", "repo_handlers")

## Getting item handlers
h <- rp$handlers()
## handlers have the same names as the items in the repo (and they
## include an handler to the repo itself).
names(h)

## Without arguments, function "item1" loads item named "item1".
i1 <- h$item1()

## Arguments can be used to call other repo functions on the item.
h$item1("info")

## After putting new data, the handlers must be refreshed.
rp$put(3, "item3", "Sample item 3", "repo_handlers")
h <- rp$handlers()
names(h)

## wiping temporary repo
unlink(rp_path, TRUE)

Description

Check whether a repository has an item

Usage

repo_has(name)

Arguments

Value

TRUE if name is in the repository, FALSE otherwise.

Description

Provides detailed information about an item.

Usage

repo_info(name = NULL, tags = NULL)

Arguments

Value

Used for side effects.

Examples

rp_path <- file.path(tempdir(), "example_repo")
rp <- repo_open(rp_path, TRUE)
rp$put(1, "item1", "Sample item 1", "info")
rp$info("item1")

## wiping temporary repo
unlink(rp_path, TRUE)

Description

lazydo searches the repo for previous execution of an expression. If a previous execution is found, the result is loaded and returned. Otherwise, the expression is executed and the result stashed.

Usage

repo_lazydo(expr, force = F, env = parent.frame())

Arguments

Details

The expression results are stashed as usual. The name of the resource is obtained by digesting the expression, so it will look like an MD5 string in the repo. Note that the expression, and not its result, will uniquely identify the item in the repo.

The new item is automatically tagged with "stash", "hide" and "lazydo".

Value

Results of the expression (either loaded or computed on the fly).

See Also

repo_stash, repo_put

Examples

rp_path <- file.path(tempdir(), "example_repo")
rp <- repo_open(rp_path, TRUE)


## First run
system.time(rp$lazydo(
    {
        Sys.sleep(1/10)
        x <- 10
    }
))

## lazydo is building resource from code.
## Cached item name is: f3c27f11f99dce20919976701d921c62
##   user  system elapsed 
##  0.004   0.000   0.108 

## Second run
system.time(rp$lazydo(
    {
        Sys.sleep(1/10)
        x <- 10
    }
))

## lazydo found precomputed resource.
##   user  system elapsed 
##  0.001   0.000   0.001 


## The item's name in the repo can be obtained as the name of the
## last item added:

l <- length(rp$entries())
resname <- rp$entries()[[l]]$name
cat(rp$entries()[[l]]$description)
## {
##    Sys.sleep(1/10)
##    x <- 10
## }
rp$rm(resname) ## single cached item cleared

## wiping temporary repo
unlink(rp_path, TRUE)

Description

Like repo_get, returns the contents of a stored item. But, unlike repo_get, loads it to the current namespace.

Usage

repo_load(names, overwrite_existing = F, env = parent.frame())

Arguments

Value

Nothing, used for side effects.

Description

If a repository does not exist at the specified location, creates a directory and stores the repository index in it. If a repository exists, the index is loaded and a repo object is built.

Arguments

Value

An object of class repo.

Examples

## Creates a new repository in a temporary directory without asking for
## confirmation.
rp_path <- file.path(tempdir(), "example_repo")
rp <- repo_open(rp_path, TRUE)
rp$put(0, "zero", "a random item", "a_tag")
rp$info()
## wiping temporary repo
unlink(rp_path, TRUE)

Description

Set repository-wide options

Usage

repo_options(...)

Arguments

Value

if optional parameters are not passed, the current options are returned

Description

The pie chart shows all repository items as pie slices of size proportional to the item sizes on disk. Items with size smaller then 5

Usage

repo_pies(...)

Arguments

Value

Used for side effects.

Examples

## Repository creation
rp_path <- file.path(tempdir(), "example_repo")
rp <- repo_open(rp_path, TRUE)

## Producing some irrelevant data of different sizes
data1 <- 1:10
data2 <- 1:length(data(1))*2
data3 <- 1:length(data(1))*3

## Putting the data in the database, specifying dependencies
rp$put(data1, "item1", "First item", "repo_pies")
rp$put(data2, "item2", "Second item", "repo_pies")
rp$put(data3, "item3", "Third item", "repo_pies")

## Showing the pie chart
rp$pies()

## wiping temporary repo
unlink(rp_path, TRUE)

Description

Show a summary of the repository contents.

Usage

repo_print(tags = NULL, tagfun = "OR", find = NULL, all = F, show = "ds")

Arguments

Details

The tagfun param specifies how to combine multiple tags when matching items. It can be either a character or a function. As a character, it can be one of OR, AND or NOT to specify that one, all or none of the tags must be matched, respectively. If it is a function, it must take two tag vectors, the first of which corresponds to tags, and return TRUE for a match, FALSE otherwise.

The find param can be any character string to be matched against any item field, including string-converted size (like "10x3").

Value

Used for side effects.

Examples

rp_path <- file.path(tempdir(), "example_repo")
rp <- repo_open(rp_path, TRUE)
rp$put(1, "item1", "Sample item 1", c("tag1", "tag2"))
rp$put(2, "item2", "Sample item 2", c("tag1", "hide"))
rp$put(3, "item3", "Sample item 3", c("tag2", "tag3"))
rp$print()
rp$print(all=TRUE)
rp$print(show="tds", all=TRUE)
rp$print(show="tds", all=TRUE, tags="tag1")
## wiping the temp repo
unlink(rp_path, TRUE)

## wiping temporary repo
unlink(rp_path, TRUE)

Description

A project item is a special item containing session information, including package dependencies. Every time a new item is stored in the repository, it will automatically be assigned to the current project, if one has been defined, and session information will be updated.

Usage

repo_project(name, description, replace = T)

Arguments

Value

Used for side effects.

Description

Download item remote content

Usage

repo_pull(name, replace = F)

Arguments

Details

Repo index files can be used as pointers to remote data. The pull function will download the actual data from the Internet, including regular items or attachment. Another use of the URL item's parameter is to attach a remote resource without downloading it.

Value

Used for side effects.

Examples

## Repository creation
rp_path <- file.path(tempdir(), "example_repo")
rp <- repo_open(rp_path, TRUE)
remote_URL <- paste0("https://github.com/franapoli/repo/blob/",
                     "untested/inst/remote_sample.RDS?raw=true")

## The following item will have remote source
rp$put("Local content", "item1", "Sample item 1", "tag",
         URL = remote_URL)
print(rp$get("item1"))

## suppressWarnings(try(rp$pull("item1"), TRUE))
 tryCatch(rp$pull("item1"),
         error = function(e)
             message("There were warnings whle accessing remote content"),
         warning = function(w)
             message("Could not download remote content")
         )
print(rp$get("item1"))

## wiping temporary repo
unlink(rp_path, TRUE)

Description

Given an R object, stores it to an RDS file in the repo root and add an associated item to the repo index, including object name, description, tags and more.

Usage

repo_put(
  obj,
  name = NULL,
  description = NULL,
  tags = NULL,
  prj = NULL,
  src = NULL,
  chunk = name,
  depends = NULL,
  replace = F,
  asattach = F,
  to = NULL,
  addversion = F,
  URL = NULL,
  checkRelations = T
)

Arguments

Details

The item name can be any string, however it should be a concise identifier, possibly without special character (could become mandatory soon). Some tags have a special meaning, like "hide" (do not show the item by default), "attachment" (the item is an attachment - this should never be set manually), "stash" (the item is a stashed item, makes the item over-writable by other "stash" items by default).

Value

Used for side effects.

See Also

get, set, attach, info

Examples

## Repository creation
rp_path <- file.path(tempdir(), "example_repo")
rp <- repo_open(rp_path, TRUE)

## Producing some irrelevant data
data1 <- 1:10
data2 <- data1 * 2
data3 <- data1 / 2

## Putting the data in the database, specifying dependencies
rp$put(
    obj = data1,
    name = "item1",
    description = "First item",
    tags = c("repo_put", "a_random_tag"),
    )
rp$put(data2, "item2", "Item dependent on item1",
    "repo_dependencies", depends="item1")
rp$put(data3, "item3", "Item dependent on item1 and item2",
    "repo_dependencies", depends=c("item1", "item2"))

print(rp)

## Creating another version of item1
data1.2 <- data1 + runif(10)
rp$put(data1.2, name = "item1", "First item with additional noise",
    tags = c("repo_put", "a_random_tag"), replace="addversion")
print(rp, all=TRUE)
rp$info("item1#1")

## wiping temporary repo
unlink(rp_path, TRUE)

Description

Relations are defined as in the dependency graph.

Usage

repo_related(names, type = "all", excludeseed = F)

Arguments

Value

A character vector of item names.

See Also

dependencies

Description

Remove item from the repo (and the disk).

Usage

repo_rm(name = NULL, tags = NULL, force = F)

Arguments

Value

Used for side effects.

Examples

rp_path <- file.path(tempdir(), "example_repo")
rp <- repo_open(rp_path, TRUE)
rp$put(1, "item1", "Sample item 1", "info")
rp$put(2, "item2", "Sample item 2", "info")
print(rp)
rp$rm("item1")
print(rp)

## wiping temporary repo
unlink(rp_path, TRUE)

Description

Show path to repo root

Usage

repo_root()

Value

character containing the path to the root of the repo.

Examples

rp_path <- file.path(tempdir(), "example_repo")
rp <- repo_open(rp_path, TRUE)
print(rp$root())

## wiping temporary repo
unlink(rp_path, TRUE)

Description

Edit an existing item.

Usage

repo_set(
  name,
  obj = NULL,
  newname = NULL,
  description = NULL,
  tags = NULL,
  prj = NULL,
  src = NULL,
  chunk = NULL,
  depends = NULL,
  addtags = NULL,
  URL = NULL,
  buildURL = NULL
)

Arguments

Value

Used for side effects.

See Also

repo_put

Examples

rp_path <- file.path(tempdir(), "example_repo")
rp <- repo_open(rp_path, TRUE)
rp$put(1, "item1", "Sample item 1", c("tag1", "tag2"))
rp$set("item1", obj=2)
print(rp$get("item1"))
rp$set("item1", description="Modified description", tags="new_tag_set")
rp$info("item1")

## wiping temporary repo
unlink(rp_path, TRUE)

Description

A very simplified call to put that only requires to specify a variable name.

Usage

repo_stash(object, rename = deparse(substitute(object)))

Arguments

Details

The name parameter is used to search the parent (or a different specified) environment for the actual object to store. Then it is also used as the item name. The reserved tags "stash" and "hide" are set. In case a stashed item by the same name already exists, it is automatically overwritten. In case a non-stashed item by the same name already exists, an error is raised. A different name can be specified through the rename parameter in such cases.

Value

Used for side effects.

See Also

repo_put, repo_lazydo

Examples

## Not run: 
rp_path <- file.path(tempdir(), "example_repo")
rp <- repo_open(rp_path, TRUE)
tempdata <- runif(10)
rp$stash(tempdata)
rp$info("tempdata")

## wiping temporary repo
unlink(rp_path, TRUE)

## End(Not run)

Description

Remove all stashed data

Usage

repo_stashclear(force = F)

Arguments

Value

Used for side effects.

See Also

repo_rm, repo_stash

Examples

## Not run: 
rp_path <- file.path(tempdir(), "example_repo")
rp <- repo_open(rp_path, TRUE)
tempdata <- runif(10)
rp$stash("tempdata")
rp$print(all=TRUE)
rp$stashclear(TRUE)

## wiping temporary repo
unlink(rp_path, TRUE)

## End(Not run)

Description

Runs a system command passing as parameter the file name containing the object associated with an item.

Usage

repo_sys(name, command)

Arguments

Value

Used for side effects.

Examples

## Repository creation
rp_path <- file.path(tempdir(), "example_repo")
rp <- repo_open(rp_path, TRUE)

## Creating a PDF file with a figure.
pdffile <- file.path(rp_path, "afigure.pdf")
pdf(pdffile)
plot(runif(30), runif(30))
dev.off()

## Attaching the PDF file to the repo
rp$attach(pdffile, "A plot of random numbers", "repo_sys")
## don't need the original PDF file anymore
file.remove(pdffile)

## Opening the stored PDF with Evince document viewer
## Not run: 
rp$sys("afigure.pdf", "evince")

## End(Not run)

## wiping temporary repo
unlink(rp_path, TRUE)

Description

Add tags to an item.

Usage

repo_tag(name = NULL, newtags, tags = NULL)

Arguments

Value

Used for side effects.

See Also

repo_untag, repo_set

Examples

rp_path <- file.path(tempdir(), "example_repo")
rp <- repo_open(rp_path, TRUE)
rp$put(1, "item1", "Sample item 1", "tag1")
rp$print(show="t")
rp$tag("item1", "tag2")
rp$print(show="t")

## wiping temporary repo
unlink(rp_path, TRUE)

Description

Shows list of all unique tags associated with any item in the repository.

Usage

repo_tags(name)

Arguments

Value

Character vector of unique tags defined in the repo.

See Also

repo_put

Examples

rp_path <- file.path(tempdir(), "example_repo")
rp <- repo_open(rp_path, TRUE)

## Putting two items with a few tags
rp$put(1, "item1", "Sample item 1",
    c("repo_tags", "tag1"))
rp$put(2, "item2", "Sample item 2",
    c("repo_tags", "tag2"))

## Looking up tags
rp$tags()

## wiping temporary repo
unlink(rp_path, TRUE)

Description

Remove tags from an item.

Usage

repo_untag(name = NULL, rmtags, tags = NULL)

Arguments

Value

Used for side effects.

See Also

repo_tag, repo_set

Examples

rp_path <- file.path(tempdir(), "example_repo")
rp <- repo_open(rp_path, TRUE)
rp$put(1, "item1", "Sample item 1", c("tag1", "tag2"))
rp$print(show="t")
rp$untag("item1", "tag2")
rp$print(show="t")

## wiping temporary repo
unlink(rp_path, TRUE)