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Merged
ypriverol merged 14 commits into from
Mar 11, 2026
Merged

Minor changes #809

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cd99f3c
Minor changes
ypriverol Mar 9, 2026
de13668
Merge branch 'dev' of https://github.com/bigbio/proteomics-sample-met…
ypriverol Mar 9, 2026
83c6ebb
Add PDF specification v1.1.0-dev
github-actions[bot] Mar 9, 2026
bc7716d
minor changes
ypriverol Mar 9, 2026
7a0de41
Merge branch 'master' of https://github.com/bigbio/proteomics-sample-…
ypriverol Mar 9, 2026
084f7e1
Merge branch 'dev' of https://github.com/bigbio/proteomics-sample-met…
ypriverol Mar 9, 2026
c6dfaa8
Add PDF specification v1.1.0-dev
github-actions[bot] Mar 9, 2026
3d86f5f
minor changes
ypriverol Mar 9, 2026
b35671a
Merge branch 'dev' of https://github.com/bigbio/proteomics-sample-met…
ypriverol Mar 9, 2026
5241654
Add PDF specification v1.1.0-dev
github-actions[bot] Mar 9, 2026
57f2f08
small change
ypriverol Mar 9, 2026
a61da80
minor changes in the example for crosslinking
ypriverol Mar 11, 2026
c9ca04c
Merge branch 'dev' of https://github.com/bigbio/proteomics-sample-met…
ypriverol Mar 11, 2026
c652716
Add PDF specification v1.1.0-dev
github-actions[bot] Mar 11, 2026
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Binary file modified psi-document/sdrf-proteomics-specification-v1.1.0-dev.pdf
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33 changes: 20 additions & 13 deletions scripts/inject-headers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -38,11 +38,11 @@ def inject_header(filepath: str, header_html: str, is_dev: bool = False) -> None
with open(filepath, 'r', encoding='utf-8') as f:
content = f.read()

# Resolve version link based on dev/stable mode
# Resolve version link: only show in dev builds (link back to stable)
if is_dev:
version_link = '<a href="/" class="version-link">Stable Version</a>'
else:
version_link = '<a href="/dev/" class="version-link">Dev Version</a>'
version_link = ''
resolved_header = header_html.replace(VERSION_LINK_PLACEHOLDER, version_link)
Comment on lines +41 to 46
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@coderabbitai coderabbitai bot Mar 9, 2026

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⚠️ Potential issue | 🟠 Major

Avoid hard-coding the Stable Version link to "/".

Every other nav URL in this script is relative, but these two injections jump to the domain root. That breaks the version switch when the docs are served from a project subpath or opened from a generated local build. Please derive the stable target from the deployment base/page depth instead of baking in "/".

Also applies to: 71-76

🤖 Prompt for AI Agents 
Verify each finding against the current code and only fix it if needed.

In `@scripts/inject-headers.py` around lines 41 - 46, The Stable Version link is
hard-coded to "/" which breaks docs served from subpaths; replace that literal
with a computed stable target derived from the deployment base or page depth
(e.g., compute a relative base like "../" repeated page_depth or use an existing
deployment_base variable if present) and use that value when building
version_link instead of "/". Update the block that sets version_link (refer to
is_dev, VERSION_LINK_PLACEHOLDER, header_html, resolved_header) to compute
stable_target = computed_base + maybe "index.html" or root of the docs site and
then set version_link = f'<a href="{stable_target}" class="version-link">Stable
Version</a>'; apply the same change to the analogous footer/footer injection
code around lines 71-76 so both injections derive the stable URL the same way.


# Add has-doc-header class to body
Expand All @@ -56,17 +56,24 @@ def inject_header(filepath: str, header_html: str, is_dev: bool = False) -> None
f.write(content)


def rewrite_version_links(filepath: str, is_dev: bool) -> None:
"""Rewrite version links in static HTML pages (index.html, quickstart.html, etc.)."""
def inject_version_link_into_static(filepath: str, is_dev: bool) -> None:
"""Inject a 'Stable Version' link into static HTML pages for dev builds."""
if not is_dev:
return # Stable builds don't show a version link

with open(filepath, 'r', encoding='utf-8') as f:
content = f.read()

if is_dev:
content = content.replace(
'<a href="/dev/" class="version-link">Dev Version</a>',
'<a href="/" class="version-link">Stable Version</a>'
)
# No change needed for stable — the source files already have /dev/ links
# Already has a version link — skip
if 'class="version-link"' in content:
return

# Insert "Stable Version" link before the GitHub link
stable_link = '<a href="/" class="version-link">Stable Version</a>'
content = content.replace(
'<a href="https://github.com/bigbio/proteomics-metadata-standard"',
stable_link + '<a href="https://github.com/bigbio/proteomics-metadata-standard"'
)

with open(filepath, 'w', encoding='utf-8') as f:
f.write(content)
Expand Down Expand Up @@ -120,13 +127,13 @@ def main():
print(f"Injecting header into: {html_file}")
inject_header(str(html_file), HEADERS['templates'], is_dev)

# Rewrite version links in static HTML pages (index.html, quickstart.html, etc.)
# Inject version link into static HTML pages for dev builds
for static_page in ["index.html", "quickstart.html", "sdrf-terms.html",
"sdrf-explorer.html", "sdrf-editor.html", "sdrf-builder.html"]:
static_file = output_dir / static_page
if static_file.exists():
print(f"Rewriting version links in: {static_file}")
rewrite_version_links(str(static_file), is_dev)
print(f"Processing version link in: {static_file}")
inject_version_link_into_static(str(static_file), is_dev)

print("Header injection complete!")

Expand Down
35 changes: 29 additions & 6 deletions site/js/sdrf-builder.js
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Expand Up @@ -45,6 +45,7 @@
affinitySubtype: null,
extraColumns: [], // columns from sdrf-terms.tsv added by user
addedOptionals: [], // optional template columns the user opted into
removedColumns: [], // recommended columns the user explicitly removed
factorValues: [] // characteristics chosen as factor values
};

Expand Down Expand Up @@ -180,6 +181,9 @@
if (req === 'optional') {
// Only include if user explicitly added it
if (state.addedOptionals.indexOf(colName) === -1) continue;
} else if (req === 'recommended') {
// Exclude if user explicitly removed it
if (state.removedColumns.indexOf(colName) !== -1) continue;
}
result.push(col2);
}
Expand Down Expand Up @@ -380,6 +384,7 @@
state.experiments = [];
state.affinitySubtype = null;
state.addedOptionals = [];
state.removedColumns = [];
state.extraColumns = [];
state.factorValues = [];

Expand Down Expand Up @@ -608,8 +613,9 @@
continue;
}

if (req === 'optional' && !includedNames[colName]) {
// Optional and not enabled -> goes in "optional" section
if ((req === 'optional' && !includedNames[colName]) ||
(req === 'recommended' && state.removedColumns.indexOf(colName) !== -1)) {
// Optional not enabled, or recommended that user removed -> "optional" section
optionalCols.push(col);
} else if (includedNames[colName] && state.extraColumns.indexOf(colName) === -1) {
// Included from template (not user-added extra)
Expand Down Expand Up @@ -734,7 +740,14 @@
item.appendChild(toggleBtn);

item.addEventListener('click', function () {
state.addedOptionals.push(col.name);
var req = col.requirement || 'optional';
if (req === 'recommended') {
// Re-add: remove from removedColumns
var idx = state.removedColumns.indexOf(col.name);
if (idx !== -1) state.removedColumns.splice(idx, 1);
} else {
state.addedOptionals.push(col.name);
}
updatePreview();
});
optDiv.appendChild(item);
Expand Down Expand Up @@ -844,6 +857,11 @@
// Remove from extra
var idx = state.extraColumns.indexOf(colName);
if (idx !== -1) state.extraColumns.splice(idx, 1);
} else if (col.requirement === 'recommended') {
// Move recommended column to removed list
if (state.removedColumns.indexOf(colName) === -1) {
state.removedColumns.push(colName);
}
} else {
// Toggle optional template column off (remove from addedOptionals)
var idx2 = state.addedOptionals.indexOf(colName);
Expand Down Expand Up @@ -896,11 +914,16 @@
var columns = resolveColumns();
if (!columns.length) return;

var names = [];
var headers = [];
var values = [];
for (var i = 0; i < columns.length; i++) {
names.push(columns[i].name);
headers.push(columns[i].name);
values.push(columns[i].example_value || '');
}
window.open('sdrf-editor.html?columns=' + encodeURIComponent(names.join(',')));

var tsv = headers.join('\t') + '\n' + values.join('\t') + '\n';
var encoded = btoa(unescape(encodeURIComponent(tsv)));
window.open('sdrf-editor.html?content=' + encodeURIComponent(encoded));
}

/* ---------------------------------------------------------------
Expand Down
1 change: 0 additions & 1 deletion site/quickstart.html
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Expand Up @@ -109,7 +109,6 @@
<a href="./sdrf-explorer.html">Explorer</a>
<a href="./sdrf-editor.html">Editor</a>
<a href="./quickstart.html" class="nav-current">Quick Start</a>
<a href="/dev/" class="version-link">Dev Version</a>
<a href="https://github.com/bigbio/proteomics-metadata-standard" target="_blank">GitHub</a>
</nav>
</div>
Expand Down
1 change: 0 additions & 1 deletion site/sdrf-builder.html
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Expand Up @@ -17,7 +17,6 @@
<a href="./index.html#tools">Tools</a>
<a href="./sdrf-explorer.html">Explorer</a>
<a href="./sdrf-editor.html">Editor</a>
<a href="/dev/" class="version-link">Dev Version</a>
<a href="https://github.com/bigbio/proteomics-metadata-standard" target="_blank">GitHub</a>
</nav>
</div>
Expand Down
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