ExternalData¶
Manage data files stored outside source tree
Use this module to unambiguously reference data files stored outside
the source tree and fetch them at build time from arbitrary local and
remote content-addressed locations. Functions provided by this module
recognize arguments with the syntax DATA{<name>} as references to
external data, replace them with full paths to local copies of those
data, and create build rules to fetch and update the local copies.
The DATA{} syntax is literal and the <name> is a full or relative path
within the source tree. The source tree must contain either a real
data file at <name> or a “content link” at <name><ext> containing a
hash of the real file using a hash algorithm corresponding to <ext>.
For example, the argument DATA{img.png} may be satisfied by either a
real img.png file in the current source directory or a img.png.md5
file containing its MD5 sum.
The ExternalData_Expand_Arguments function evaluates DATA{}
references in its arguments and constructs a new list of arguments:
ExternalData_Expand_Arguments(
<target> # Name of data management target
<outVar> # Output variable
[args...] # Input arguments, DATA{} allowed
)
It replaces each DATA{} reference in an argument with the full path of
a real data file on disk that will exist after the <target> builds.
The ExternalData_Add_Test function wraps around the CMake
add_test() command but supports DATA{} references in
its arguments:
ExternalData_Add_Test(
<target> # Name of data management target
... # Arguments of add_test(), DATA{} allowed
)
It passes its arguments through ExternalData_Expand_Arguments and then
invokes the add_test() command using the results.
The ExternalData_Add_Target function creates a custom target to
manage local instances of data files stored externally:
ExternalData_Add_Target(
<target> # Name of data management target
)
It creates custom commands in the target as necessary to make data
files available for each DATA{} reference previously evaluated by
other functions provided by this module. A list of URL templates may
be provided in the variable ExternalData_URL_TEMPLATES using the
placeholders %(algo) and %(hash) in each template. Data fetch
rules try each URL template in order by substituting the hash
algorithm name for %(algo) and the hash value for %(hash).
The following hash algorithms are supported:
%(algo) <ext> Description
------- ----- -----------
MD5 .md5 Message-Digest Algorithm 5, RFC 1321
SHA1 .sha1 US Secure Hash Algorithm 1, RFC 3174
SHA224 .sha224 US Secure Hash Algorithms, RFC 4634
SHA256 .sha256 US Secure Hash Algorithms, RFC 4634
SHA384 .sha384 US Secure Hash Algorithms, RFC 4634
SHA512 .sha512 US Secure Hash Algorithms, RFC 4634
Note that the hashes are used only for unique data identification and download verification.
Example usage:
include(ExternalData)
set(ExternalData_URL_TEMPLATES "file:///local/%(algo)/%(hash)"
"file:////host/share/%(algo)/%(hash)"
"http://data.org/%(algo)/%(hash)")
ExternalData_Add_Test(MyData
NAME MyTest
COMMAND MyExe DATA{MyInput.png}
)
ExternalData_Add_Target(MyData)
When test MyTest runs the DATA{MyInput.png} argument will be
replaced by the full path to a real instance of the data file
MyInput.png on disk. If the source tree contains a content link
such as MyInput.png.md5 then the MyData target creates a real
MyInput.png in the build tree.
The DATA{} syntax can be told to fetch a file series using the form
DATA{<name>,:}, where the : is literal. If the source tree
contains a group of files or content links named like a series then a
reference to one member adds rules to fetch all of them. Although all
members of a series are fetched, only the file originally named by the
DATA{} argument is substituted for it. The default configuration
recognizes file series names ending with #.ext, _#.ext, .#.ext,
or -#.ext where # is a sequence of decimal digits and .ext is
any single extension. Configure it with a regex that parses <number>
and <suffix> parts from the end of <name>:
ExternalData_SERIES_PARSE = regex of the form (<number>)(<suffix>)$
For more complicated cases set:
ExternalData_SERIES_PARSE = regex with at least two () groups
ExternalData_SERIES_PARSE_PREFIX = <prefix> regex group number, if any
ExternalData_SERIES_PARSE_NUMBER = <number> regex group number
ExternalData_SERIES_PARSE_SUFFIX = <suffix> regex group number
Configure series number matching with a regex that matches the
<number> part of series members named <prefix><number><suffix>:
ExternalData_SERIES_MATCH = regex matching <number> in all series members
Note that the <suffix> of a series does not include a hash-algorithm
extension.
The DATA{} syntax can alternatively match files associated with the
named file and contained in the same directory. Associated files may
be specified by options using the syntax
DATA{<name>,<opt1>,<opt2>,...}. Each option may specify one file by
name or specify a regular expression to match file names using the
syntax REGEX:<regex>. For example, the arguments:
DATA{MyData/MyInput.mhd,MyInput.img} # File pair
DATA{MyData/MyFrames00.png,REGEX:MyFrames[0-9]+\\.png} # Series
will pass MyInput.mha and MyFrames00.png on the command line but
ensure that the associated files are present next to them.
The DATA{} syntax may reference a directory using a trailing slash and
a list of associated files. The form DATA{<name>/,<opt1>,<opt2>,...}
adds rules to fetch any files in the directory that match one of the
associated file options. For example, the argument
DATA{MyDataDir/,REGEX:.*} will pass the full path to a MyDataDir
directory on the command line and ensure that the directory contains
files corresponding to every file or content link in the MyDataDir
source directory.
The variable ExternalData_LINK_CONTENT may be set to the name of a
supported hash algorithm to enable automatic conversion of real data
files referenced by the DATA{} syntax into content links. For each
such <file> a content link named <file><ext> is created. The
original file is renamed to the form .ExternalData_<algo>_<hash> to
stage it for future transmission to one of the locations in the list
of URL templates (by means outside the scope of this module). The
data fetch rule created for the content link will use the staged
object if it cannot be found using any URL template.
The variable ExternalData_OBJECT_STORES may be set to a list of local
directories that store objects using the layout <dir>/%(algo)/%(hash).
These directories will be searched first for a needed object. If the
object is not available in any store then it will be fetched remotely
using the URL templates and added to the first local store listed. If
no stores are specified the default is a location inside the build
tree.
The variable ExternalData_SOURCE_ROOT may be set to the highest source
directory containing any path named by a DATA{} reference. The
default is CMAKE_SOURCE_DIR. ExternalData_SOURCE_ROOT and
CMAKE_SOURCE_DIR must refer to directories within a single source
distribution (e.g. they come together in one tarball).
The variable ExternalData_BINARY_ROOT may be set to the directory to
hold the real data files named by expanded DATA{} references. The
default is CMAKE_BINARY_DIR. The directory layout will mirror that of
content links under ExternalData_SOURCE_ROOT.
Variables ExternalData_TIMEOUT_INACTIVITY and
ExternalData_TIMEOUT_ABSOLUTE set the download inactivity and absolute
timeouts, in seconds. The defaults are 60 seconds and 300 seconds,
respectively. Set either timeout to 0 seconds to disable enforcement.