Add vaRRI visualization, reproducible ZIP exports and parameter tabs

.github/workflows/build-wasm.yml

@@ -30,8 +30,19 @@ jobs:
       - uses: actions/setup-python@v6
         with:
           python-version: '3.12'
+      - name: Test dependency download integrity and cache recovery
+        run: |
+          python scripts/wasm/test-downloads.py
+          python scripts/wasm/test-vienna-release.py
       - name: Test input, worker lifecycle and CSV handling
         run: npm test --prefix webinterface
+      - name: Resolve newest stable ViennaRNA 2.x release and checksum
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: |
+          python scripts/wasm/vienna-release.py --latest > "$RUNNER_TEMP/vienna-release.json"
+          cat "$RUNNER_TEMP/vienna-release.json"
+          echo "WASM_VIENNA_RELEASE=$RUNNER_TEMP/vienna-release.json" >> "$GITHUB_ENV"
       - name: Cross-compile dependencies and IntaRNA
         run: bash scripts/wasm/build.sh
       - name: Check real WASM predictions against the native reference

ChangeLog

@@ -14,6 +14,10 @@
 
 ## Interface and handling
 
+- add selected-interaction vaRRI embeds and reproducible all-output ZIP downloads
+  to the browser interface; compact parameters into accessible tabs and update
+  the Freiburg group header and full-width result/footer notes (PR #287 review)
+
 - extend the browser interface with vaRRI styling, prediction/evaluation tasks,
   multi-FASTA, start indices, CLI parameter groups, selectable CSV columns and
   additional output previews/downloads; label pair-relative differences mfe Δ
@@ -80,6 +84,14 @@
 
 ## Technical changes and Optimizations
 
+- build WASM with ViennaRNA 2.7.2 locally and the newest stable 2.x in CI;
+  verify published archive checksums, isolate versioned caches and retain
+  selected dependency provenance and notices (PR #292 review)
+
+- BUGFIX : restore WASM dependency downloads using the pinned official ViennaRNA
+  release asset; verify downloads before caching and recover invalid caches
+  (PR #291)
+
 - annotate inherited virtual methods/destructors with override, preserve compiled
   WASM asset provenance through staging, and expand protocol/browser validation
   for the PR #287 review
@@ -241,6 +253,62 @@ energies, restricted partition sums, and trackers.
 ################################################################################  
 ################################################################################
 
+261022 Alexander Mitrofanov
+ * scripts/wasm/{vienna-release.py,vienna-release.json}, build.sh
+   + Resolve the newest stable ViennaRNA >=2.7.2 and <3 from all official GitHub
+     release pages in CI; require its release tarball and published SHA-256.
+   * Pin 2.7.2 for reproducible local builds and accept saved release manifests.
+     Isolate RNAlib sources/installations and IntaRNA objects by archive identity
+     and keep Boost/zlib in a separate prefix to prevent reuse or include-path
+     shadowing of libraries/headers from another release (PR #292).
+ * scripts/wasm/patch-vienna.py
+   - Remove the dlib 19.24 compatibility patch; ViennaRNA 2.7.2 bundles dlib 20.0.
+ * scripts/wasm/{write-build-info.mjs,stage.sh,smoke-protocol.mjs,test-browser.py}
+   * Record the selected archive URL/checksum, check the compiled ViennaRNA
+     version, stage matching dependency notices and test actual version exports.
+ * scripts/wasm/test-vienna-release.py, .github/workflows/build-wasm.yml
+   + Cover numeric version selection, pagination, major-3/prerelease exclusion,
+     missing/invalid asset metadata, API failures, manifest validation and
+     rejection of compiled engines with a stale ViennaRNA version.
+ * webinterface/docs/step1-wasm-compilation.md
+   * Document latest-2.x CI selection, pinned local reproduction, versioned
+     caches, current bundled dlib and archive provenance.
+
+261022 Alexander Mitrofanov
+ * scripts/wasm/{build,download}.sh
+   * Use the official GitHub ViennaRNA 2.7.0 release asset and pin its SHA-256;
+     the university endpoint returned a short HTTP 200 text response, failing
+     the WASM build before compilation (PR #291).
+   + Verify archives before caching, discard invalid cached responses and remove
+     failed partial downloads so rerunning a build can recover automatically.
+ * scripts/wasm/test-downloads.py, .github/workflows/build-wasm.yml
+   + Test verified-cache reuse, invalid-cache recovery, checksum failures,
+     HTTP errors and truncated transfers against a local HTTP server in CI.
+ * webinterface/docs/step1-wasm-compilation.md
+   * Document the release source, archive verification and download regression
+     command, including recovery behavior for failed or outdated caches.
+
+261022 Alexander Mitrofanov
+ * webinterface/{archive,visualization}.js
+   + Build local UTF-8 ZIPs with normalized FASTA, compiled version provenance,
+     portable parameter files, selected CSV, auxiliary inputs and all outputs;
+     include separate replay configurations for native text report modes.
+   + Construct selected-row vaRRI URLs from full target/query sequences, native
+     dot-bracket output, names and signed indices, preserving strand direction.
+ * webinterface/{app,results,protocol}.js, index.html, styles.css
+   + Add row selection, embedded vaRRI/full-viewer link and Download ZIP action;
+     preserve completed-run inputs and clear exports/viewer when inputs change.
+   * Replace folded groups with keyboard-accessible tabs and compact parameter
+     grids; link Bioinformatics - University of Freiburg to the group website
+     and remove artificial width limits from table/footer notes.
+ * scripts/wasm/{stage.sh,smoke-protocol.mjs,test-browser.py}
+   * Stage the new modules; verify byte-identical replay through fresh engines
+     and browser tab/selection/ZIP behavior in Chromium and Firefox.
+ * webinterface/tests/export.test.mjs, README.md, webinterface/docs/*
+   + Cover coordinate/identity mapping, effective settings and archive inputs;
+     document replay commands, external visualization and browser limitations
+     (https://github.com/BackofenLab/IntaRNA/pull/287#issuecomment-6321503136).
+
 261021 Alexander Mitrofanov
  * src/IntaRNA/*.h
    * Mark 194 inherited virtual methods and 45 derived destructors override;

README.md

@@ -6,6 +6,7 @@
 seeding of interaction sites**
 
 Predict short RNA pairs or evaluate supplied structures locally with the [browser interface](https://backofenlab.github.io/IntaRNA/webinterface/).
+Select an interaction to view it in vaRRI, or download a ZIP with inputs, compiled versions, reproducible parameters and all outputs.
 See the [WebAssembly build instructions](webinterface/docs/step1-wasm-compilation.md) and
 [interface/deployment notes](webinterface/docs/step4-results-and-deployment.md).
 

scripts/wasm/build.sh

@@ -5,34 +5,42 @@ repo=$(cd "$(dirname "$0")/../.." && pwd)
 build=${WASM_BUILD_DIR:-"$repo/build-wasm"}
 mkdir -p "$build"
 build=$(cd "$build" && pwd)
-prefix="$build/deps"
+# Keep legacy RNAlib headers out of Boost's -I path: ordinary -I searches take
+# precedence over the -isystem ViennaRNA paths produced by IntaRNA's configure.
+prefix="$build/deps/common"
 jobs=${JOBS:-2}
-for tool in emcc em++ emar emranlib emconfigure emmake curl pkg-config node; do
+for tool in emcc em++ emar emranlib emconfigure emmake curl pkg-config node python3; do
   command -v "$tool" >/dev/null || { echo "Missing tool: $tool" >&2; exit 1; }
 done
 mkdir -p "$build/downloads" "$build/sources" "$prefix" "$build/site/wasm"
 fetch() {
-  local url=$1 name=$2 checksum=$3
-  if [[ ! -f "$build/downloads/$name" ]]; then
-    curl --fail --location --retry 3 "$url" -o "$build/downloads/$name.part"
-    mv "$build/downloads/$name.part" "$build/downloads/$name"
-  fi
-  echo "$checksum  $build/downloads/$name" | sha256sum --check -
+  bash "$repo/scripts/wasm/download.sh" "$1" "$build/downloads/$2" "$3"
 }
 fetch https://zlib.net/fossils/zlib-1.3.1.tar.gz zlib-1.3.1.tar.gz \
   9a93b2b7dfdac77ceba5a558a580e74667dd6fede4585b91eefb60f03b72df23
 fetch https://archives.boost.io/release/1.87.0/source/boost_1_87_0.tar.bz2 boost_1_87_0.tar.bz2 \
   af57be25cb4c4f4b413ed692fe378affb4352ea50fbe294a11ef548f4d527d89
-fetch https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_7_x/ViennaRNA-2.7.0.tar.gz ViennaRNA-2.7.0.tar.gz \
-  9a99fd68ed380894defb4d5e6a8a2871629270028cdf7f16f0a05da6e8c71473
+# CI supplies the newest stable 2.x manifest; local builds use the checked-in pin.
+read -r vienna_version vienna_url vienna_sha256 < <(
+  python3 "$repo/scripts/wasm/vienna-release.py" --fields \
+    --manifest "${WASM_VIENNA_RELEASE:-$repo/scripts/wasm/vienna-release.json}"
+)
+echo "Building ViennaRNA $vienna_version (SHA-256 $vienna_sha256)"
+fetch "$vienna_url" "ViennaRNA-$vienna_version.tar.gz" "$vienna_sha256"
+# Separate source, installed RNAlib and IntaRNA objects by archive identity so
+# changing the release cannot reuse headers, libraries or objects from an old one.
+vienna_id="vienna-$vienna_version-$vienna_sha256"
+vienna_prefix="$build/deps/$vienna_id"
+vienna_sources="$build/sources/$vienna_id"
+intarna_build="$build/intarna-$vienna_id"
 
 # Keep pkg-config searches inside the WASM prefix, including configure probes.
-export PKG_CONFIG_LIBDIR="$prefix/lib/pkgconfig"
+export PKG_CONFIG_LIBDIR="$vienna_prefix/lib/pkgconfig:$prefix/lib/pkgconfig"
 export PKG_CONFIG_PATH="$PKG_CONFIG_LIBDIR"
 export CFLAGS='-O3 -fexceptions'
 export CXXFLAGS='-O3 -fexceptions'
-export CPPFLAGS="-I$prefix/include"
-export LDFLAGS="-L$prefix/lib -fexceptions"
+export CPPFLAGS="-I$vienna_prefix/include -I$prefix/include"
+export LDFLAGS="-L$vienna_prefix/lib -L$prefix/lib -fexceptions"
 if [[ ! -f "$prefix/lib/libz.a" ]]; then
   tar -xzf "$build/downloads/zlib-1.3.1.tar.gz" -C "$build/sources"
   (cd "$build/sources/zlib-1.3.1"
@@ -52,27 +60,26 @@ if [[ ! -f "$prefix/.boost-1.87.0-js-exceptions-complete" ]]; then
      -sZLIB_LIBPATH="$prefix/lib" --prefix="$prefix" install)
   touch "$prefix/.boost-1.87.0-js-exceptions-complete"
 fi
-if [[ ! -f "$prefix/lib/libRNA.a" ]]; then
-  tar -xzf "$build/downloads/ViennaRNA-2.7.0.tar.gz" -C "$build/sources"
-  (cd "$build/sources/ViennaRNA-2.7.0"
-   CPPFLAGS="$CPPFLAGS -I$PWD/src" emconfigure ./configure --host=wasm32-unknown-emscripten --prefix="$prefix" \
+if [[ ! -f "$vienna_prefix/.complete" ]]; then
+  mkdir -p "$vienna_sources"
+  tar -xzf "$build/downloads/ViennaRNA-$vienna_version.tar.gz" -C "$vienna_sources"
+  (cd "$vienna_sources/ViennaRNA-$vienna_version"
+   CPPFLAGS="$CPPFLAGS -I$PWD/src" emconfigure ./configure --host=wasm32-unknown-emscripten --prefix="$vienna_prefix" \
      --disable-shared --enable-static --disable-openmp --disable-pthreads \
      --disable-lto --disable-simd --disable-vectorize --disable-mpfr \
      --without-svm --without-gsl --without-swig --without-perl --without-python \
      --without-doc --without-cla --without-check --without-kinfold \
      --without-forester --without-rnalocmin --without-rnaxplorer
-   # Backport dlib's upstream char32_t typedef for modern libc++ char_traits.
-   # Only the downloaded dependency is patched; RNAlib algorithms are unchanged.
-   python3 "$repo/scripts/wasm/patch-vienna.py" "$PWD"
    emmake make -C src/ViennaRNA -j "$jobs"
    emmake make -C src/ViennaRNA install
    emmake make install-pkgconfigDATA)
+  touch "$vienna_prefix/.complete"
 fi
 
 # Legacy Autoconf probes declare exit()/inflateEnd() with the wrong signatures,
 # which wasm-ld rejects. Verify real dependency APIs before caching those probes.
-em++ -std=c++23 -O2 -fexceptions -I"$prefix/include" \
-  "$repo/scripts/wasm/dependency-probe.cpp" -L"$prefix/lib" \
+em++ -std=c++23 -O2 -fexceptions -I"$vienna_prefix/include" -I"$prefix/include" \
+  "$repo/scripts/wasm/dependency-probe.cpp" -L"$vienna_prefix/lib" -L"$prefix/lib" \
   -lboost_filesystem -lboost_system -lboost_program_options -lboost_regex \
   -lboost_iostreams -lboost_serialization -lRNA -lz -o "$build/dependency-probe.js"
 node "$build/dependency-probe.js"
@@ -83,15 +90,15 @@ export ac_cv_lib_boost_regex_exit=yes
 export ac_cv_lib_boost_iostreams_exit=yes
 export ac_cv_lib_z_inflateEnd=yes
 # RNAlib's .pc embeds a native-only -Wl,-fno-lto; this is a static WASM build.
-export VRNA_LIBS="-L$prefix/lib -lRNA -lm"
+export VRNA_LIBS="-L$vienna_prefix/lib -lRNA -lm"
 
 # Use the native Autotools source lists and CLI entry point, with a JS output.
 (cd "$repo" && bash autotools-init.sh)
-mkdir -p "$build/intarna"
-(cd "$build/intarna"
- CXXFLAGS="$CXXFLAGS -Werror=inconsistent-missing-override" CPPFLAGS="-I$build/intarna/src -I$repo/src $CPPFLAGS" emconfigure "$repo/configure" --host=wasm32-unknown-emscripten \
+mkdir -p "$intarna_build"
+(cd "$intarna_build"
+ CXXFLAGS="$CXXFLAGS -Werror=inconsistent-missing-override" CPPFLAGS="-I$intarna_build/src -I$repo/src $CPPFLAGS" emconfigure "$repo/configure" --host=wasm32-unknown-emscripten \
    --disable-multithreading --disable-log-coloring --with-mdspan=kokkos \
-   --with-vrna="$prefix" --with-boost="$prefix" \
+   --with-vrna="$vienna_prefix" --with-boost="$prefix" \
    --with-boost-libdir="$prefix/lib" --with-zlib="$prefix"
  emmake make -C src -j "$jobs" EXEEXT=.js \
    LDFLAGS="$LDFLAGS -sMODULARIZE=1 -sEXPORT_ES6=1 -sEXPORT_NAME=createIntaRNA -sENVIRONMENT=web,worker,node -sINVOKE_RUN=0 -sEXIT_RUNTIME=1 -sEXPORTED_RUNTIME_METHODS=FS,callMain -sALLOW_MEMORY_GROWTH=1 -sMAXIMUM_MEMORY=1073741824 -sSTACK_SIZE=8388608"
@@ -101,5 +108,6 @@ mkdir -p "$build/intarna"
 printf '{"type":"module"}\n' > "$build/site/wasm/package.json"
 node "$repo/scripts/wasm/write-build-info.mjs" "$repo" "$build/site" \
   "$(emcc -dumpversion)" "$(git -C "$repo" rev-parse HEAD)" \
-  "$(git -C "$repo" status --porcelain --untracked-files=no)"
+  "$(git -C "$repo" status --porcelain --untracked-files=no)" \
+  "$vienna_version" "$vienna_url" "$vienna_sha256"
 echo "WASM assets: $build/site/wasm"

scripts/wasm/download.sh

@@ -0,0 +1,23 @@
+#!/usr/bin/env bash
+# Cache only verified dependency archives; recover from invalid cached responses.
+set -euo pipefail
+url=$1
+destination=$2
+checksum=$3
+
+# Verify existing archives too, including caches from earlier build scripts.
+if [[ -f "$destination" ]]; then
+  if printf '%s  %s\n' "$checksum" "$destination" | sha256sum --check --status; then
+    echo "$destination: OK (cached)"
+    exit 0
+  fi
+  echo "Discarding invalid cached archive: $destination" >&2
+  rm -- "$destination"
+fi
+
+# Never promote HTTP error pages or incomplete transfers to the download cache.
+partial="$destination.part"
+trap 'rm -f -- "$partial"' EXIT
+curl --fail --location --retry 3 "$url" -o "$partial"
+printf '%s  %s\n' "$checksum" "$partial" | sha256sum --check -
+mv -- "$partial" "$destination"