fe02c55d26614f1d5059c884fb2594f9b4d5ad50
mspeir
  Wed Aug 12 08:02:19 2026 -0700
singleCellSignalsPeaks: point at the hub build's new home, fix the file-copy script

The hub build now lives in the cellBrowser repo under ucsc/allTracksHub, so the makeDocs
link there instead of a personal work dir. HUB_BUILD in these scripts is the build's
output dir, not its code; comments say so now, paths unchanged.

copySingleCellSignalsPeaksFiles.py was silently copying nothing: it compared a whole line
against "parent <composite>", but stanzas are now indented and read "parent <composite>
off". Now dedents, matches the first token, and refuses to run on zero subtracks. Dry runs
give 925 hg38 / 587 mm10, none missing.

refs #37914

diff --git src/hg/makeDb/scripts/singleCellSignalsPeaks/copySingleCellSignalsPeaksFiles.py src/hg/makeDb/scripts/singleCellSignalsPeaks/copySingleCellSignalsPeaksFiles.py
index 9181b286aea..5b9a839ad63 100644
--- src/hg/makeDb/scripts/singleCellSignalsPeaks/copySingleCellSignalsPeaksFiles.py
+++ src/hg/makeDb/scripts/singleCellSignalsPeaks/copySingleCellSignalsPeaksFiles.py
@@ -1,98 +1,108 @@
 #!/usr/bin/env python3
 """
 Copy the source data files for the native singleCellSignalsPeaks track into the
 genome's bed directory, mirroring each file's served relative path (Redmine
 #37820 for hg38, #37914 for mm10).
 
 For the given assembly it reads the hub build's main signal-&-peaks composite
 (cellBrowser<Asm>) stanzas, and for every subtrack copies the source file
 (resolved from the hub manifest by served relative path) to
   /hive/data/genomes/<asm>/bed/singleCellSignalsPeaks/<served-relpath>
 The served subpath is preserved on purpose: some peak-file basenames repeat
 across datasets, so a flat directory would clobber them, and keeping the subpath
 lets the /gbdb/<asm>/bbi/singleCellSignalsPeaks symlink resolve every bigDataUrl.
 
 It also copies the composite's facet metadata to
   <bed>/singleCellSignalsPeaks_metadata.tsv   (the track's metaDataUrl target).
 
 Usage:
   copySingleCellSignalsPeaksFiles.py [--assembly hg38|mm10] [--dry-run]
 """
 import re, os, shutil, argparse
 from urllib.parse import urlparse
 
-# Where the hub build writes manifest.tsv. That machinery builds the whole Cell Browser
-# super hub, not just this track, so it lives outside the kent tree; override with
-# HUB_BUILD when it moves (or pass --manifest).
+# Where the hub build writes manifest.tsv -- its OUTPUT dir, not its code. The build
+# itself lives in the cellBrowser repo (ucsc/allTracksHub):
+#   https://github.com/ucscGenomeBrowser/cellBrowser/tree/develop/ucsc/allTracksHub
+# Its output dir is set there by CBHUB_OUT; keep this default in step with it (or pass
+# --manifest).
 HUB_BUILD = os.environ.get(
     "HUB_BUILD", "/hive/users/mspeir/claude/cell-browser/all-tracks-hub-build")
 TRACK = "singleCellSignalsPeaks"
 
 def load_relpath_to_abs(manifest, asm):
     m = {}
     with open(manifest) as fh:
         hdr = fh.readline().rstrip("\n").split("\t")
         ai, ui, asmi = hdr.index("abs_path"), hdr.index("track_url"), hdr.index("assembly")
         for line in fh:
             f = line.rstrip("\n").split("\t")
             if len(f) <= max(ai, ui, asmi) or f[asmi] != asm:
                 continue
             m[urlparse(f[ui]).path.lstrip("/")] = f[ai]
     return m
 
 def main():
     ap = argparse.ArgumentParser()
     ap.add_argument("--assembly", default="hg38", choices=["hg38", "mm10"])
     ap.add_argument("--stanzas")
     ap.add_argument("--manifest", default=os.path.join(HUB_BUILD, "manifest.tsv"))
     ap.add_argument("--dry-run", action="store_true")
     args = ap.parse_args()
 
     asm = args.assembly
     hub_composite = "cellBrowser" + asm.capitalize()
     stanzas = args.stanzas or os.path.join(HUB_BUILD, "stanzas/%s.trackDb.txt" % asm)
     beddir = "/hive/data/genomes/%s/bed/%s" % (asm, TRACK)
     rel2abs = load_relpath_to_abs(args.manifest, asm)
 
     copied = missing = total = 0
     nbytes = 0
     misses = []
     for s in re.split(r"\n\s*\n", open(stanzas).read().strip()):
-        lines = s.splitlines()
-        parent = next((l for l in lines if l.startswith("parent ")), "").strip()
-        if parent != "parent " + hub_composite:
+        # Dedent, and match the parent's first token rather than the whole line. The hub
+        # stanzas are indented to show their hierarchy and each child says
+        # "parent <composite> off", so an anchored whole-line compare matched nothing and
+        # this copied zero files without complaining.
+        lines = [l.lstrip() for l in s.splitlines()]
+        parent = next((l for l in lines if l.startswith("parent ")), "").split()
+        if len(parent) < 2 or parent[1] != hub_composite:
             continue
         bdu = next((l for l in lines if l.strip().startswith("bigDataUrl ")), None)
         if not bdu:
             continue
         total += 1
         rel = urlparse(bdu.split(None, 1)[1].strip()).path.lstrip("/")
         src = rel2abs.get(rel)
         if not src or not os.path.exists(src):
             missing += 1
             misses.append(rel)
             continue
         dst = os.path.join(beddir, rel)
         if not args.dry_run:
             os.makedirs(os.path.dirname(dst), exist_ok=True)
             if not (os.path.exists(dst) and os.path.getsize(dst) == os.path.getsize(src)):
                 shutil.copy2(src, dst)
         copied += 1
         nbytes += os.path.getsize(src)
 
     meta_src = os.path.join(HUB_BUILD, "meta", "%s.metadata.tsv" % asm)
     meta_dst = os.path.join(beddir, "%s_metadata.tsv" % TRACK)
     if not args.dry_run and os.path.exists(meta_src):
         os.makedirs(beddir, exist_ok=True)
         shutil.copy2(meta_src, meta_dst)
 
+    if total == 0:
+        raise SystemExit("ERROR: no subtracks of %s found in %s. Has the hub stanza "
+                         "layout changed? Copying nothing is never right here."
+                         % (hub_composite, stanzas))
     print("assembly=%s composite=%s: subtracks=%d copied=%d missing=%d  ~%.1f GB%s"
           % (asm, hub_composite, total, copied, missing, nbytes / 1e9,
              "  (dry-run)" if args.dry_run else "  -> " + beddir))
     if misses:
         print("MISSING %d source files:" % len(misses))
         for r in misses[:25]:
             print("  " + r)
 
 if __name__ == "__main__":
     main()