ExternalData

Manage data files stored outside source tree

Introduction

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.

For example:

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.

Module Functions

ExternalData_Expand_Arguments

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.

ExternalData_Add_Test

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.

ExternalData_Add_Target

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. Data files may be fetched from one of the URL templates specified in the ExternalData_URL_TEMPLATES variable, or may be found locally in one of the paths specified in the ExternalData_OBJECT_STORES variable.

Module Variables

The following variables configure behavior. They should be set before calling any of the functions provided by this module.

ExternalData_BINARY_ROOT

The ExternalData_BINARY_ROOT variable 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.

ExternalData_CUSTOM_SCRIPT_<key>

Specify a full path to a .cmake custom fetch script identified by <key> in entries of the ExternalData_URL_TEMPLATES list. See Custom Fetch Scripts.

ExternalData_LINK_CONTENT

The ExternalData_LINK_CONTENT variable 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 real data files named by expanded DATA{} references may be made available under ExternalData_BINARY_ROOT using symbolic links on some platforms. The ExternalData_NO_SYMLINKS variable may be set to disable use of symbolic links and enable use of copies instead.

ExternalData_OBJECT_STORES

The ExternalData_OBJECT_STORES variable 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.

ExternalData_SERIES_PARSE
ExternalData_SERIES_PARSE_PREFIX
ExternalData_SERIES_PARSE_NUMBER
ExternalData_SERIES_PARSE_SUFFIX
ExternalData_SERIES_MATCH

See Referencing File Series.

ExternalData_SOURCE_ROOT

The ExternalData_SOURCE_ROOT variable 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).

ExternalData_TIMEOUT_ABSOLUTE

The ExternalData_TIMEOUT_ABSOLUTE variable sets the download absolute timeout, in seconds, with a default of 300 seconds. Set to 0 to disable enforcement.

ExternalData_TIMEOUT_INACTIVITY

The ExternalData_TIMEOUT_INACTIVITY variable sets the download inactivity timeout, in seconds, with a default of 60 seconds. Set to 0 to disable enforcement.

ExternalData_URL_ALGO_<algo>_<key>

Specify a custom URL component to be substituted for URL template placeholders of the form %(algo:<key>), where <key> is a valid C identifier, when fetching an object referenced via hash algorithm <algo>. If not defined, the default URL component is just <algo> for any <key>.

ExternalData_URL_TEMPLATES

The ExternalData_URL_TEMPLATES may be set to provide a list of of 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). Alternatively one may use %(algo:<key>) with ExternalData_URL_ALGO_<algo>_<key> variables to gain more flexibility in remote URLs.

Referencing Files

Referencing Single Files

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.

Referencing File Series

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.

Referencing Associated Files

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.

Referencing Directories

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. In order to match associated files in subdirectories, specify a RECURSE: option, e.g. DATA{MyDataDir/,RECURSE:,REGEX:.*}.

Hash Algorithms

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.

Custom Fetch Scripts

When a data file must be fetched from one of the URL templates specified in the ExternalData_URL_TEMPLATES variable, it is normally downloaded using the file(DOWNLOAD) command. One may specify usage of a custom fetch script by using a URL template of the form ExternalDataCustomScript://<key>/<loc>. The <key> must be a C identifier, and the <loc> must contain the %(algo) and %(hash) placeholders. A variable corresponding to the key, ExternalData_CUSTOM_SCRIPT_<key>, must be set to the full path to a .cmake script file. The script will be included to perform the actual fetch, and provided with the following variables:

ExternalData_CUSTOM_LOCATION

When a custom fetch script is loaded, this variable is set to the location part of the URL, which will contain the substituted hash algorithm name and content hash value.

ExternalData_CUSTOM_FILE

When a custom fetch script is loaded, this variable is set to the full path to a file in which the script must store the fetched content. The name of the file is unspecified and should not be interpreted in any way.

The custom fetch script is expected to store fetched content in the file or set a variable:

ExternalData_CUSTOM_ERROR

When a custom fetch script fails to fetch the requested content, it must set this variable to a short one-line message describing the reason for failure.