Merge pull request #809 from bigbio/dev

Minor changes

Author: ypriverol

examples/PXD042173/PXD042173.sdrf.tsv

@@ -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)
 
     # Add has-doc-header class to body
@@ -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)
@@ -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!")
 

psi-document/sdrf-proteomics-specification-v1.1.0-dev.pdf

@@ -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
     };
 
@@ -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);
         }
@@ -380,6 +384,7 @@
         state.experiments = [];
         state.affinitySubtype = null;
         state.addedOptionals = [];
+        state.removedColumns = [];
         state.extraColumns = [];
         state.factorValues = [];
 
@@ -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)
@@ -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);
@@ -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);
@@ -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));
     }
 
     /* ---------------------------------------------------------------

scripts/inject-headers.py

@@ -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>

site/js/sdrf-builder.js

@@ -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>