679b48855a32f8ea1e1ea8ca3c095a0c2c7f6c7a max Tue Sep 8 10:08:41 2026 -0700 detailsScript: add a scatterPlot plot type, and use it for pcLAI Clicking a pcLAI window now shows where that window sits in the ancestry space it was placed in: a scatterplot of the 1000 Genomes reference haplotypes with the window's own PCA coordinate and its segment's coordinate marked on it. The numbers were already on the details page and told a reader almost nothing. New plot type scatterPlot (hg/js/hgc.scatterPlot.js), driven the same way as histogram. Background points come from a JSON or TSV file named by dataUrl and may carry a category, which colors them and builds a legend, and a label, which is shown on mouseover. The cloud is drawn on a canvas, since these files hold thousands of points and that many <circle> elements make the page crawl; axes and the highlighted points stay SVG on top. Point lookup for the mouseover goes through a cell index so a large file stays smooth. Two additions serve every plot type, not just this one: - exportFields, a config key listing further bigBed fields whose values are passed to the module as a fieldValues object. Without it a plot needing two coordinates would need them packed into one field, and pcLAI keeps them in pca and pcaSegment. Only fields that exist in the bigBed are exported, at most 32, and the JSON types are checked rather than asserted because jsonListVal and jsonStringVal errAbort and this JSON is written by a hub. - a config key ending in Url is treated as a file, by the convention trackSettingIsFile() already uses, and a relative one is resolved against the track's own bigDataUrl. The module does not fetch it directly; it asks hgTrackUi for it, the route facetedComposite uses for its metadata. That checks the canonicalized path against the hubs on the cart and reads it with udc, so a hub-relative path works even for a hub loaded from a local path (the GenArk /gbdb hubs), no CORS header is needed, and a file outside a connected hub cannot be read. Verified that /etc/passwd, file://, a dot-dot escape, an unattached hub and an unrelated host are all refused with 400. When the session has file caching off, hgc now exports udcTimeout the way hgTrackUi does and the module POSTs, so the browser cannot answer from cache. Fixes a crash reachable from any hub: "detailsScript.<plotType>.<field> null" segfaulted hgc, because jsonObjectVal returns NULL for a JSON null and the hash routines dereference it. This hit the shipped histogram type too. trackDbSettingsGen.py stopped reading a setting's description at the first "Example:" paragraph and never read <ul> at all, so it dropped everything after the first example and every list item. That silently truncated 226 of the 264 descriptions, including spectrum's minGrayLevel/scoreMin/scoreMax bullets, and would have dropped this whole scatterPlot section. It now skips the Example label instead of stopping, and folds list items in. No setting loses a word and none gains or loses an example. pcLAI wiring: the background file is the authors' published reference panel (github.com/AI-sandbox/hprc-pclai reference_pca_metadata.tsv), converted by hprc2annotMakePclaiRefPanel.py -- 3122 haplotypes, 21 populations, 94 KB, one file for the collection since it is the reference space rather than per-assembly data. The four values pcaSegment takes across all 460 assemblies turn out to be the four continental cluster centres, so the highlighted segment dot always lands on one of them. genark: addContrib now rewrites a "...Url" inside a detailsScript value the same way it rewrites bigDataUrl, and symlinks the collection's shared root-level data files next to the docs, so contrib/<name>/<file> resolves in the deeper GenArk layout. It writes the alpha tier only, leaving the assembly's default hub alone, and clears any unmarked copy of the collection's stanzas that the assembly build baked in, which would otherwise leave the hub declaring each track twice. refs #35415 diff --git src/hg/htdocs/goldenPath/help/trackDb/trackDbSettingsGen.py src/hg/htdocs/goldenPath/help/trackDb/trackDbSettingsGen.py index 3a3e857e1d6..cd6c6795498 100644 --- src/hg/htdocs/goldenPath/help/trackDb/trackDbSettingsGen.py +++ src/hg/htdocs/goldenPath/help/trackDb/trackDbSettingsGen.py @@ -1,302 +1,317 @@ #!/usr/bin/env python3 """Generate machine-readable trackDb settings data from the trackDb help docs. trackDbLibrary.shtml gives each setting's name, types, description and example. trackDbHub.v3.html says which ones hubs support, and at what level, by which table the row sits in. --import read those two pages, write trackDbSettings.yaml --json read trackDbSettings.yaml, write trackDbSettings.json Run "make settings" after editing the docs. Do not hand-edit the yaml: --import rewrites it, so corrections go in this script. Longer term the yaml should be the source the reader HTML is built from too; today it only feeds the json. """ import sys import os import re import json import argparse from bs4 import BeautifulSoup import yaml HERE = os.path.dirname(os.path.abspath(__file__)) HUB_VERSION = "v3" LIB = os.path.join(HERE, "trackDbLibrary.shtml") HUB = os.path.join(HERE, "trackDbHub.%s.html" % HUB_VERSION) YAML_OUT = os.path.join(HERE, "trackDbSettings.yaml") JSON_OUT = os.path.join(HERE, "trackDbSettings.json") # Stanzas a setting can appear in. hub.txt and genomes.txt are stanzas of their own, so a # trackDb "common" setting spans the four track roles, not all six. ROLE_ORDER = ["hub", "genome", "super", "composite", "view", "leaf"] ALL_ROLES = ["super", "composite", "view", "leaf"] # Doc sections named for their anchor because the keyword collides with a trackDb setting # of the same name. The keyword is what goes in a hub file, so map them back. DOC_NAME_TO_KEYWORD = { "hubShortLabel": "shortLabel", "hubLongLabel": "longLabel", "hubGenome": "genome", "trackDbFile": "trackDb", "groupsFile": "groups", "type_for_hubs": "type", } # The docs use HTML entities that decode to non-ASCII punctuation. Fold them: "format" is # a syntax template someone pastes into a hub file, and the generated files are ASCII. UNICODE_TO_ASCII = { "\u00a0": " ", # nbsp "\u2013": "-", # ndash "\u2014": "-", # mdash "\u2018": "'", # lsquo "\u2019": "'", # rsquo "\u201c": '"', # ldquo "\u201d": '"', # rdquo "\u2026": "...", # hellip } def toAscii(text): """Fold the docs' punctuation to ASCII, warning about anything left over.""" for uni, plain in UNICODE_TO_ASCII.items(): text = text.replace(uni, plain) extra = sorted(set(c for c in text if ord(c) > 126)) if extra: print("warning: no ASCII spelling for %s, add it to UNICODE_TO_ASCII" % ", ".join("%r %s" % (c, hex(ord(c))) for c in extra), file=sys.stderr) return text def prettify(tableId): """Turn a settingsTable id into a human category label.""" return tableId.replace("_-_", " - ").replace("_", " ").strip() def roleHints(tableId): """Guess which stanzas a table's settings apply to, from its id.""" t = tableId.lower() if "supertrack" in t: return ["super"] if "view" in t and "composite" in t: return ["view"] if "composite" in t or "faceted" in t or "subgroup" in t: return ["composite"] if "aggregate" in t or "overlay" in t: return ["composite", "view", "leaf"] if "common" in t: return list(ALL_ROLES) if "hub_file" in t: return ["hub"] if "genomes_file" in t: return ["genome"] if "deprecated" in t: return [] # unknown, doImport falls back to the types return ["leaf"] # type-specific tables (bam, bigBed, bigWig, vcfTabix, ...) def contextOf(tableId): """Which file a table's settings go in: hub.txt, genomes.txt, or a trackDb file.""" t = tableId.lower() if "genomes_file" in t: return "genomes" if "hub_file" in t: return "hub" return "trackDb" def firstSentence(text, cap=160): """First sentence, length-capped, for the one-line summary.""" text = re.sub(r"\s+", " ", text).strip() if not text: return "" m = re.search(r"\.(\s|$)", text) s = text[:m.start() + 1] if m else text if len(s) > cap: s = s[:cap - 3].rstrip() + "..." return s def parseLibrary(): """name -> {types, format, required, description, summary, examples}.""" with open(LIB, encoding="utf-8") as f: soup = BeautifulSoup(f.read(), "html.parser") blurbs = {} for span in soup.find_all("span", class_="types"): div = span.parent classes = div.get("class") or [] if not classes: continue name = classes[0] if name.endswith("_intro") or name.endswith("_example"): continue types = [c for c in span.get("class", []) if not c.startswith("types")] if not types: types = ["all"] fmtDiv = div.find("div", class_="format") fmtCode = fmtDiv.find("code") if fmtDiv else None fmt = toAscii(fmtCode.get_text(" ", strip=True)) if fmtCode else name req = div.find("p", class_="isRequired") reqText = req.get_text(" ", strip=True).lower() if req else "" required = "yes" in reqText or "for hubs" in reqText + # Walk p and ul in document order. Stopping at the first "Example" paragraph + # would lose every later paragraph, which matters for a setting that documents + # more than one variant, so the label is skipped rather than ended on. List + # items carry real content, so <ul> is folded in as well. descParts = [] - for p in div.find_all("p"): - if "isRequired" in (p.get("class") or []): + + def addPart(txt, prefix=""): + # The source wraps paragraphs over several lines, so squeeze each block to + # one line; blocks are then joined by newlines to keep them apart. + txt = re.sub(r"\s+", " ", txt).strip() + if txt: + descParts.append(prefix + txt) + + for el in div.find_all(["p", "ul"]): + if el.name == "ul": + for li in el.find_all("li"): + addPart(li.get_text(" ", strip=True), "- ") continue - txt = p.get_text(" ", strip=True) + if "isRequired" in (el.get("class") or []): + continue + txt = el.get_text(" ", strip=True) if txt.lower().startswith("example"): - break - if txt: - descParts.append(txt) - description = toAscii(re.sub(r"\s+", " ", " ".join(descParts)).strip()) + continue + addPart(txt) + description = toAscii("\n".join(descParts).strip()) examples = [] for pre in div.find_all("pre"): ex = toAscii(pre.get_text().strip()) if ex: examples.append(ex) blurbs[name] = { "types": types, "format": fmt, "required": required, "description": description, "summary": firstSentence(description), "examples": examples, } return blurbs def parseHubSpec(): """Walk the hub spec tables in order. Returns (order, home, hints): setting names in document order, home[name] = {category, context, level}, hints[name] = set of roles. """ with open(HUB, encoding="utf-8") as f: soup = BeautifulSoup(f.read(), "html.parser") # Scan the whole document rather than the #specification subtree: html.parser # closes that div early at a malformed tag, hiding the later container tables. order = [] home = {} hints = {} for table in soup.find_all("table", class_="settingsTable"): tid = table.get("id", "") if tid == "toc": continue category = prettify(tid) context = contextOf(tid) tHints = roleHints(tid) for td in table.find_all("td"): classes = td.get("class") or [] if not classes: continue name = classes[0] code = td.find("code") if code is None: continue level = None for c in (code.get("class") or []): if c.startswith("level-"): level = c[len("level-"):] if name not in home: order.append(name) home[name] = {"category": category, "context": context, "level": level} hints[name] = set() hints[name].update(tHints) return order, home, hints def doImport(): blurbs = parseLibrary() order, home, hints = parseHubSpec() entries = [] missing = [] for name in order: b = blurbs.get(name) if b is None: missing.append(name) continue info = home[name] roles = [r for r in ROLE_ORDER if r in hints[name]] if not roles and info["context"] == "trackDb": if b["types"] == ["all"]: # A copy, or safe_dump writes yaml aliases to one shared list. roles = list(ALL_ROLES) else: roles = ["leaf"] entries.append({ "name": name, "types": b["types"], "roles": roles, "category": info["category"], "context": info["context"], "level": info["level"], "required": b["required"], "summary": b["summary"], "description": b["description"], "format": b["format"], "examples": b["examples"], }) with open(YAML_OUT, "w", encoding="utf-8") as f: f.write("# Generated by trackDbSettingsGen.py --import, which rewrites the whole file.\n") f.write("# Edit the trackDb help docs instead, then run 'make settings'.\n") f.write("# 'roles' is a guess from which doc table a setting sits in; check the\n") f.write("# container-only ones.\n\n") yaml.safe_dump(entries, f, sort_keys=False, width=100) print("imported %d settings -> %s" % (len(entries), YAML_OUT)) if missing: print(" (%d hub rows had no library blurb, skipped): %s" % (len(missing), ", ".join(missing))) def doJson(): with open(YAML_OUT, encoding="utf-8") as f: entries = yaml.safe_load(f) categories = [] settings = [] for e in entries: if not e["roles"]: continue cat = e["category"] if cat not in categories: categories.append(cat) example = e["examples"][0] if e["examples"] else "" # "fmt" is the syntax to fill in, "ex" the doc's example of it filled in. settings.append({ "key": DOC_NAME_TO_KEYWORD.get(e["name"], e["name"]), "category": cat, "roles": e["roles"], "types": "all" if e["types"] == ["all"] else e["types"], "level": e["level"], "fmt": e["format"], "ex": example, "desc": e["summary"], }) out = {"version": HUB_VERSION, "categories": categories, "settings": settings} with open(JSON_OUT, "w", encoding="utf-8") as f: json.dump(out, f, indent=1) f.write("\n") print("wrote %d settings in %d categories -> %s" % (len(settings), len(categories), JSON_OUT)) def main(): ap = argparse.ArgumentParser(description=__doc__) ap.add_argument("--import", dest="doImport", action="store_true", help="write trackDbSettings.yaml from the help docs") ap.add_argument("--json", dest="doJson", action="store_true", help="write trackDbSettings.json from trackDbSettings.yaml") args = ap.parse_args() if not (args.doImport or args.doJson): ap.error("specify --import and/or --json") if args.doImport: doImport() if args.doJson: doJson() if __name__ == "__main__": main()