fix(live): stop a child's page telling which result is closed through ids, second genes and fixed panels

CHANGELOG.md

@@ -5,6 +5,7 @@ Each release's notes. From 1.0.0 on, a major or minor release has hand-written n
 ## Unreleased
 
 - The family page now keeps a child's results to act on closed, as the child's own page does, and what it shows of a child no longer depends on which result is closed or where it lies. While a child has a result still closed, or the page cannot read the child's results, these close for that child, one box each: the painting's grandparents (every stretch drawn from its parent alone), the chromosome map image, all de novo and compound-het rows, the child's medicines and HLA cells in the side by side, and the carrier screen of a couple the child is part of. Each "Show the result" opens one result; the places come back once the last one is opened, and a reload closes them again. While the results cannot be read, each box opens only its own place. On a child's page, a copy-number dot and a card's fact that name a closed result's gene now close with it too, on a phone in the card's line as well. `results.json` adds `veil.spans`, `veil.facts` and `veil.widget`; nothing is renamed or removed. The veil is still a browser veil: `results.json` and `family.json` hold every row.
+- A child's page no longer tells which result to act on is closed. A closed finding's card, its place in the page and the address carry a handle (`#f/closed-2`) instead of its id, which names the gene and variant; the address never holds a closable finding's id, closed (`#f/closed-<n>`) or opened (`#f/opened-<n>`), so no history entry keeps it, and any other `#f/<x>` on such a page, a closed result's id or nothing, lands on the first closed finding, so a guessed id tells nothing. The home page links a child's closed result to the child's report, not to the finding's own page. A closed structural variant now closes the rows and findings that name any of its genes, not only the first. The cards whose rows are the same genes for everyone (known mobile element insertions, repeat expansions, VNtyper, Lp(a), CHIP, the copy numbers, CPIC, CYP2D6, HLA, Locityper, the traits panel, the blood groups) close whole while any result is closed, behind one box, and so do their own findings (a medicine gene, a CHIP call) and the lead's words on them, the ClinVar card's lines for the known deep intronic sites, the carrier list's two-hit line and the callability card's rows, all together; a row or line closes with a result only when it names its gene as a gene symbol (never a prose word, an ontology id or a unit such as `5 MB`), and the polygenic score card is never tagged; a card's note on its closed rows no longer counts them. `results.json` gains `veil.panels`, the tag `*panel*` in `veil.lines`, `veil.rows`, `veil.findings` and `veil.lead`, a `genes` list on each structural-variant finding, and one `veil.spans` row per gene; nothing is renamed or removed.
 - Step 40, the 23andMe and AncestryDNA raw-data files, now runs on the Rust `og` binary: `og consumer export`, `og consumer build-sites` and `og consumer check` replace `bin/export_consumer.py`. On a synthetic gVCF of 552 MB (32 million records) with 617,044 sites it takes about 2 s and 43 MB in a Linux container on 4 cores, where the Python took 30 s and 660 MB; the files hold the same rows. `setup.sh --consumer-sites` reads dbSNP on 4 cores without the grep pass. The zips are now the same bytes for the same day (`--date`, else `SOURCE_DATE_EPOCH`, else today). Fixes: a call of three or more alleles stops the export with the site, instead of a file the strict reader refuses; two dbSNP records of one rsID at one position have their ALT alleles joined before the strand test; a bad site row or an unreadable zip is reported with the file and line instead of a traceback; a good export removes the `.txt` files a failed one left. The musl builds of `og` use the mimalloc allocator, which keeps a long multi-threaded read at its live memory. Step 40 needs `og`: `scripts/setup.sh <genome_dir>` builds it, and `scripts/setup.sh --og` builds only it.
 
 - Steps 21, 32 and 9b (and the CYRIUS, PYPGX and STRANGER_RFC1 modules) now run the CYP2D6 depth check and the RFC1 motif count with `og`, and `bin/cyp2d6_depth_check.py` and `bin/rfc1_motif.py` are gone. A run that reaches these steps needs the binary: run `./scripts/setup.sh --og` once after setup and after each pull; without it the step stops with `og is not built`. The output files, their names and formats do not change; in CI, every e2e case that runs these steps in bash checks `og` against the deleted Python, byte for byte.

assets/live/finding.js

@@ -83,9 +83,18 @@
     var tags = (r.veil && r.veil.findings) || {};
     function tagOf(x) { var t = tags[x.id]; return t && t !== x.id ? t : null; }
     // Opening this finding opens it and the result it names, nothing else: another result keeps its own veil.
+    // A finding of a fixed-panel card (tag PANEL, bin/live_results.py FIXED_PANELS) names no result: it stays closed
+    // while any result to act on is, whichever, as on the person page.
+    var PANEL = '*panel*';
     var opened = {};
-    if (draw.open) { opened[f.id] = true; if (tagOf(f)) { opened[tagOf(f)] = true; } }
-    function shut(x) { return child && (x.level === 'act' ? !opened[x.id] : !!tagOf(x) && !opened[tagOf(x)]); }
+    if (draw.open) { opened[f.id] = true; if (tagOf(f) && tagOf(f) !== PANEL) { opened[tagOf(f)] = true; } }
+    function actShut() { return (r.findings || []).some(function (x) { return x.level === 'act' && !opened[x.id]; }); }
+    function shut(x) {
+      if (!child) { return false; }
+      if (x.level === 'act') { return !opened[x.id]; }
+      var t = tagOf(x);
+      return t === PANEL ? !opened[x.id] && actShut() : !!t && !opened[t];
+    }
     // Closed: no title, gene or variant anywhere on the page (its title, crumb, cover, rail) until opened.
     var closed = shut(f);
     var title = !closed ? f.title : f.level === 'act' ? 'A result to act on' : 'A finding about a result to act on';

assets/live/home.js

@@ -192,7 +192,8 @@
     });
     items.sort(function (a, b) { return order[a.f.level] - order[b.f.level]; });
     items.slice(0, 6).forEach(function (x) {
-      var a = el('a', { href: x.r.url + 'finding/' + encodeURIComponent(x.f.id) + '/' });
+      // A child's closed result links to the run's page, never to its own page: its id names its gene and variant.
+      var a = el('a', { href: x.r.url + (closedRuns[x.r.name] && x.f.level === 'act' ? '' : 'finding/' + encodeURIComponent(x.f.id) + '/') });
       var who = el('span', { 'class': 'who' });
       var pc = el('span', { 'class': 'pc' }, x.r.name);
       if (colourOf[x.r.name]) { pc.style.setProperty('--pcol', colourOf[x.r.name]); }

assets/live/map.js

@@ -106,7 +106,8 @@
   // --- the figure ---------------------------------------------------------------------------------------
   // create({url, veil(id, gated) -> 'open'|'closed'|'opened', now(id) -> shown at this moment, open(id),
   // close(id), known(id) -> a finding of the page's results, closed() -> the ids of the results to act on the
-  // page keeps closed at this moment, stepDone(step) -> ended at this moment, fallback() -> rows}): one figure
+  // page keeps closed at this moment, stepDone(step) -> ended at this moment, href(id) -> the address of a finding
+  // the page opened (never its id on a child's page), fallback() -> rows}): one figure
   // per page. The page calls refresh(key) on each of its redraws; a new key
   // fetches the document again and keeps the camera.
   function create(opts) {
@@ -910,7 +911,7 @@
       inSection = inSection.filter(function (id) { return stateOf(id) !== 'closed' && opts.title && opts.title(id); });
       inSection.forEach(function (id) {
         var c = el('div', { 'class': 'gm-chip opened', 'data-opened': 'section' });
-        add(c, add(el('span', {}, 'Opened in its section: '), el('a', { href: '#f/' + id }, opts.title(id))));
+        add(c, add(el('span', {}, 'Opened in its section: '), el('a', { href: '#f/' + (opts.href ? opts.href(id) : id) }, opts.title(id))));
         add(c, button('Close it again', function () { confirming = null; opts.close(id); keyTo(); }));
         add(chips, c);
       });