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ENH: Migrate data to IPFS
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This improves reliability, addressing InsightSoftwareConsortium#395, but also the contributor
experience, maintainability, and sustainability.
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thewtex committed Nov 11, 2022
1 parent 06cc158 commit 9db5974
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2 changes: 1 addition & 1 deletion .gitattributes
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Expand Up @@ -12,4 +12,4 @@

# ExternalData content links must have LF newlines
*.md5 crlf=input
*.sha512 crlf=input
*.cid crlf=input
2 changes: 1 addition & 1 deletion .github/labeler.yml
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Expand Up @@ -83,7 +83,7 @@ type:Python notebook:

type:Data:
files:
- ".*.sha512"
- ".*.cid"

type:Infrastructure:
files:
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1,202 changes: 1,202 additions & 0 deletions CMake/ExternalData.cmake

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6 changes: 6 additions & 0 deletions CMake/ExternalData_config.cmake.in
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set(ExternalData_OBJECT_STORES "@ExternalData_OBJECT_STORES@")
set(ExternalData_URL_TEMPLATES "@ExternalData_URL_TEMPLATES@")
set(ExternalData_TIMEOUT_INACTIVITY "@ExternalData_TIMEOUT_INACTIVITY@")
set(ExternalData_TIMEOUT_ABSOLUTE "@ExternalData_TIMEOUT_ABSOLUTE@")
set(ExternalData_NO_SYMLINKS "@ExternalData_NO_SYMLINKS@")
@_ExternalData_CONFIG_CODE@
59 changes: 51 additions & 8 deletions CMake/ITKSphinxExamplesExternalData.cmake
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include(ExternalData)
get_filename_component(_ITKExternalData_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH)
include(${_ITKExternalData_DIR}/ExternalData.cmake)

if(NOT ExternalData_OBJECT_STORES)
# Use ExternalData_OBJECT_STORES from environment as default.
Expand All @@ -20,17 +21,59 @@ list(APPEND ExternalData_OBJECT_STORES
"${CMAKE_SOURCE_DIR}/.ExternalData"
)

set(ITK_SPHINX_EXAMPLES_DATA_RELEASED_ROOT_CID bafybeicjaaz3xi2qso3kdirmy5ixoxegvfp3bm7o44ytoh6egj5m6wgeuu)
set(ExternalData_URL_ALGO_CID_lower cid)
set(ExternalData_URL_TEMPLATES "" CACHE STRING
"Additional URL templates for the ExternalData CMake script to look for testing data. E.g.
file:///var/bigharddrive/%(algo)/%(hash)")
mark_as_advanced(ExternalData_URL_TEMPLATES)
list(APPEND ExternalData_URL_TEMPLATES
# Data published on GitHub Pages
"https://insightsoftwareconsortium.github.io/ITKTestingData/%(algo)/%(hash)"
if(NOT ITK_FORBID_DOWNLOADS)
list(APPEND ExternalData_URL_TEMPLATES
# Local IPFS gateway
"http://127.0.0.1:8080/ipfs/%(hash)"

# Data published on Girder
"https://data.kitware.com:443/api/v1/file/hashsum/%(algo)/%(hash)/download"
)
# Released data rsync'd to Kitware's Apache web server
"https://itk.org/files/ExternalData/%(algo)/%(hash)"

# Restricted gateway with released data
"https://itk.mypinata.cloud/ipfs/${ITK_SPHINX_EXAMPLES_DATA_RELEASED_ROOT_CID}/Objects/CID/%(hash)"

# New data on web3.storage
"https://w3s.link/ipfs/%(hash)"

# Released data on web3.storage
"https://${ITK_SPHINX_EXAMPLES_DATA_RELEASED_ROOT_CID}.ipfs.w3s.link/Objects/CID/%(hash)"

# Released data on estuary.tech
"https://${ITK_SPHINX_EXAMPLES_DATA_RELEASED_ROOT_CID}.ipfs.dweb.link/Objects/CID/%(hash)"

# Gateway for arbitrary new files, uploaded to web3.storage
"https://dweb.link/ipfs/%(hash)"

# Protocol Labs gateway
"https://ipfs.io/ipfs/%(hash)"

# Cloudflare gateway
"https://cloudflare-ipfs.com/ipfs/%(hash)"

# DataLad repository on gin.g-node.org
"https://gin.g-node.org/InsightSoftwareConsortium/ITKSphinxExamplesData/raw/main/Objects/CID/%(hash)"
)
endif()

# Tell ExternalData commands to transform raw files to content links.
set(ExternalData_LINK_CONTENT SHA512)
# TODO: Condition this feature on presence of our pre-commit hook.
set(ExternalData_LINK_CONTENT CID)

# Emscripten currently has difficulty reading symlinks.
if(EMSCRIPTEN)
set(ExternalData_NO_SYMLINKS 1)
endif()

# Match series of the form <base>.<ext>, <base>.<n>.<ext> such that <base> may
# end in a (test) number that is not part of any series numbering.
set(ExternalData_SERIES_PARSE "()(\\.[^./]*)$")
set(ExternalData_SERIES_MATCH "(\\.[0-9]+)?")

# Sometimes we want to download very large files.
set(ExternalData_TIMEOUT_ABSOLUTE 900)
2 changes: 1 addition & 1 deletion CMake/ITKSphinxExamplesMacros.cmake
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Expand Up @@ -113,7 +113,7 @@ function(compare_to_baseline)
endif()

file(GLOB baseline_image ${CMAKE_CURRENT_SOURCE_DIR}/${LOCAL_COMPARISON_EXAMPLE_NAME}/${LOCAL_COMPARISON_BASELINE_PREFIX}.*)
string(REPLACE .sha512 "" baseline_image "${baseline_image}")
string(REPLACE .cid "" baseline_image "${baseline_image}")
get_filename_component(baseline_image_file "${baseline_image}" NAME)
set(baseline_image "${CMAKE_CURRENT_BINARY_DIR}/${LOCAL_COMPARISON_EXAMPLE_NAME}/${baseline_image_file}")

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4 changes: 2 additions & 2 deletions CMakeLists.txt
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Expand Up @@ -125,12 +125,12 @@ set(content_links)
# corresponding locations in the binary tree.
foreach(_dir ${_RootSubDirs})
file(GLOB_RECURSE ${_dir}_content_links
RELATIVE "${ITKSphinxExamples_SOURCE_DIR}" "${_dir}/*.sha512")
RELATIVE "${ITKSphinxExamples_SOURCE_DIR}" "${_dir}/*.cid")
set(content_links ${content_links} ${${_dir}_content_links})
endforeach()

foreach(link ${content_links})
string(REGEX REPLACE "\\.sha512$" "" link ${link})
string(REGEX REPLACE "\\.cid$" "" link ${link})
ExternalData_Expand_Arguments(ITKSphinxExamplesData
link_location
DATA{${link}}
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5 changes: 2 additions & 3 deletions Utilities/CreateDownloadableArchive.py
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Expand Up @@ -43,7 +43,6 @@
for path in files_to_copy_to_html_output:
shutil.copy2(path, html_output_dir)


# archives for users to download from the website.
files_for_archive = files_to_copy_to_html_output

Expand All @@ -66,9 +65,9 @@
files_for_archive = files_for_archive[1:]
files_for_archive.append(archive_cmakelist)

inputs = glob.glob(os.path.join(example_dir, "*.sha512"))
inputs = glob.glob(os.path.join(example_dir, "*.cid"))
for path in inputs:
files_for_archive.append(path[:-7])
files_for_archive.append(path[:-4])

# Remove duplicates.
files_for_archive = set(files_for_archive)
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