open-biohacking-data / build /build_release.ps1
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Update mirror for v1.5.0 interoperability and reproducibility release
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param(
[string]$Root = (Split-Path -Parent $PSScriptRoot)
)
$ErrorActionPreference = "Stop"
$identityPath = Join-Path $Root "project_identity.json"
$packagePath = Join-Path $Root "datapackage.json"
if (-not (Test-Path $identityPath)) {
throw "project_identity.json not found."
}
if (-not (Test-Path $packagePath)) {
throw "datapackage.json not found."
}
$identity = Get-Content $identityPath -Raw | ConvertFrom-Json
$package = Get-Content $packagePath -Raw | ConvertFrom-Json
$projectVersion = $identity.release.project_version
$datasetVersion = $identity.release.dataset_version
$releaseStatus = $identity.release.release_status
$releaseDoi = $identity.release.release_doi
$conceptDoi = $identity.release.concept_doi
if ($projectVersion -ne "1.5.0") {
throw "Expected project version 1.5.0 but found $projectVersion"
}
if ($datasetVersion -ne "1.2") {
throw "Expected canonical dataset version 1.2 but found $datasetVersion"
}
if ($releaseStatus -ne "published") {
throw "Expected release status published but found $releaseStatus"
}
if ($releaseDoi -ne "10.5281/zenodo.21862535") {
throw "Published v1.5 release DOI must equal 10.5281/zenodo.21862535."
}
$stageRoot = Join-Path $Root "build\generated"
$stage = Join-Path $stageRoot "v1.5.0"
if (Test-Path $stageRoot) {
Remove-Item $stageRoot -Recurse -Force
}
New-Item -ItemType Directory -Force -Path $stage | Out-Null
$textExtensions = @(
".json",
".jsonld",
".jsonl",
".csv",
".md",
".txt",
".cff",
".ps1",
".yml",
".yaml"
)
function Copy-CanonicalFile {
param(
[string]$Source,
[string]$Destination
)
$destinationDirectory = Split-Path -Parent $Destination
if (-not (Test-Path $destinationDirectory)) {
New-Item -ItemType Directory -Force -Path $destinationDirectory | Out-Null
}
$extension = [System.IO.Path]::GetExtension($Source).ToLowerInvariant()
if ($textExtensions -contains $extension) {
$text = Get-Content $Source -Raw
$text = $text.Replace("`r`n", "`n").Replace("`r", "`n")
[System.IO.File]::WriteAllText(
$Destination,
$text,
[System.Text.UTF8Encoding]::new($false)
)
}
else {
Copy-Item $Source $Destination -Force
}
}
function Copy-CanonicalFolder {
param(
[string]$RelativeFolder
)
$sourceFolder = Join-Path $Root $RelativeFolder
if (-not (Test-Path $sourceFolder)) {
throw "Required source folder missing: $RelativeFolder"
}
Get-ChildItem $sourceFolder -Recurse -File | ForEach-Object {
$relativePath = $_.FullName.Substring($sourceFolder.Length).TrimStart("\")
$destination = Join-Path (Join-Path $stage $RelativeFolder) $relativePath
Copy-CanonicalFile -Source $_.FullName -Destination $destination
}
}
$coreFiles = @(
"README.md",
"CHANGELOG.md",
"RELEASE_NOTES_v1.5.md",
"LICENSE_DATA.txt",
"CITATION.cff",
"DEPLOYMENT_CHECKLIST.md",
"VALIDATION_SUMMARY.txt",
"WEBSITE_PUBLICATION_MAP.md",
"VERSION_HISTORY.md",
"KNOWN_LIMITATIONS.md",
"METADATA_CORRECTION_2026-08-07.md",
"project_metadata.json",
"project_identity.json",
"supersession_registry.json",
"provenance.generated.json",
"datapackage.json",
"DATA_DICTIONARY.md",
"catalog.jsonld",
"ro-crate-metadata.json",
"manifest.json",
"ai-reference.md",
"llms.txt"
)
foreach ($file in $coreFiles) {
$source = Join-Path $Root $file
if (-not (Test-Path $source)) {
throw "Required source file missing: $file"
}
Copy-CanonicalFile `
-Source $source `
-Destination (Join-Path $stage $file)
}
$folders = @(
"data",
"schemas",
"methodology"
)
foreach ($folder in $folders) {
Copy-CanonicalFolder -RelativeFolder $folder
}
$toolingFiles = @(
"build/generate_interoperability.ps1",
"build/generate_catalog_jsonld.ps1",
"build/generate_ro_crate.ps1",
"build/generate_jsonl.ps1",
"build/generate_project_identity.ps1",
"build/generate_supersession_registry.ps1",
"build/generate_provenance.ps1",
"validation/validate_project_metadata.ps1"
)
foreach ($file in $toolingFiles) {
$source = Join-Path $Root $file
$destination = Join-Path $stage ("tooling/" + $file)
if (-not (Test-Path $source)) {
throw "Required tooling file missing: $file"
}
Copy-CanonicalFile -Source $source -Destination $destination
}
$jsonErrors = @()
Get-ChildItem $stage -Recurse -File |
Where-Object {
$_.Extension -eq ".json" -or $_.Extension -eq ".jsonld"
} |
ForEach-Object {
try {
Get-Content $_.FullName -Raw | ConvertFrom-Json | Out-Null
}
catch {
$jsonErrors += $_.FullName
}
}
$jsonlErrors = @()
$jsonlRecordCount = 0
Get-ChildItem $stage -Recurse -File -Filter "*.jsonl" |
ForEach-Object {
$jsonlFile = $_.FullName
$lineNumber = 0
Get-Content $jsonlFile | ForEach-Object {
$lineNumber++
if ([string]::IsNullOrWhiteSpace($_)) {
return
}
try {
$_ | ConvertFrom-Json | Out-Null
$script:jsonlRecordCount++
}
catch {
$script:jsonlErrors += "${jsonlFile}:$lineNumber"
}
}
}
if ($jsonErrors.Count -gt 0 -or $jsonlErrors.Count -gt 0) {
Write-Host ""
Write-Host "RELEASE BUILD FAILED"
Write-Host "--------------------"
foreach ($file in $jsonErrors) {
Write-Host "FAIL JSON:" $file
}
foreach ($record in $jsonlErrors) {
Write-Host "FAIL JSONL:" $record
}
exit 1
}
$hashLines = Get-ChildItem $stage -Recurse -File |
Where-Object {
$_.Name -ne "BUILD_MANIFEST_SHA256.txt"
} |
ForEach-Object {
$relative = $_.FullName.Substring($stage.Length).TrimStart("\").Replace("\", "/")
$hash = (Get-FileHash $_.FullName -Algorithm SHA256).Hash.ToLowerInvariant()
"$hash $relative"
} |
Sort-Object
$manifestOut = Join-Path $stage "BUILD_MANIFEST_SHA256.txt"
[System.IO.File]::WriteAllText(
$manifestOut,
(($hashLines -join "`n") + "`n"),
[System.Text.UTF8Encoding]::new($false)
)
$packageFileCount = (
Get-ChildItem $stage -Recurse -File
).Count
Write-Host ""
Write-Host "V1.5 RELEASE BUILD PASSED"
Write-Host "-------------------------------"
Write-Host "Project version:" $projectVersion
Write-Host "Dataset version:" $datasetVersion
Write-Host "Release status:" $releaseStatus
Write-Host "Release DOI:" $(if ($null -eq $releaseDoi) { "NULL" } else { $releaseDoi })
Write-Host "Concept DOI:" $conceptDoi
Write-Host "Data Package resources:" $package.resources.Count
Write-Host "JSONL records:" $jsonlRecordCount
Write-Host "JSON parse errors:" $jsonErrors.Count
Write-Host "JSONL parse errors:" $jsonlErrors.Count
Write-Host "Package files:" $packageFileCount
Write-Host "Generated package:"
Write-Host $stage
Write-Host "Build manifest:"
Write-Host $manifestOut
exit 0