+
+"""Shared CopomuS ranking and tabular output helpers."""
+
+import csv
+
+
+def calculate_ranks(mutations, measure_ids):
+ """Populate total and per-measure ranks after mutations were sorted."""
+ rank = 1
+ mutations[0].ranks['total'] = rank
+ for index in range(1, len(mutations)):
+ if mutations[index - 1] < mutations[index]:
+ rank += 1
+ mutations[index].ranks['total'] = rank
+
+ for measure_index, measure_id in enumerate(measure_ids):
+ rank = 1
+ measures = [(mutation.measures[measure_index], index)
+ for index, mutation in enumerate(mutations)]
+ measures.sort(key=lambda entry: entry[0])
+ mutations[measures[0][1]].ranks[measure_id] = rank
+ for index in range(1, len(measures)):
+ measure, mutation_index = measures[index]
+ if measures[index - 1][0] < measure:
+ rank += 1
+ mutations[mutation_index].ranks[measure_id] = rank
+
+
+def table(mutations):
+ """Return the stable CopomuS header and rows for ranked mutations."""
+ headers = [column for measure in mutations[0].measures
+ for column in ([f'{measure.id}_rank']
+ + [f'{measure.id}_{key}' for key in measure.score])]
+ header = ['mutation', 'rank', 'qIndex', 'tIndex', 'bpWildtype', 'bpMutated', *headers]
+ rows = []
+ for mutation in mutations:
+ values = []
+ for measure in mutation.measures:
+ values.append(mutation.ranks[measure.id])
+ values.extend('NA' if value is None else value for value in measure.score.values())
+ rows.append([str(mutation), mutation.ranks['total'], mutation.query_n,
+ mutation.target_n, mutation.bp_ww, mutation.bp_mm, *values])
+ return header, rows
+
+
+def write_csv(mutations, handle, delimiter='\t'):
+ """Write ranked mutations with deterministic UTF-8/LF-compatible CSV."""
+ writer = csv.writer(handle, delimiter=delimiter, lineterminator='\n')
+ header, rows = table(mutations)
+ writer.writerow(header)
+ writer.writerows(rows)
diff --git a/python/tests/test_copomus.py b/python/tests/test_copomus.py
index 11ffcfc3..0e4ff5d8 100644
--- a/python/tests/test_copomus.py
+++ b/python/tests/test_copomus.py
@@ -1,7 +1,9 @@
"""CopomuS regressions for coordinates, mutation selection, profiles and ranking."""
import csv
+import asyncio
import io
+import json
from pathlib import Path
import sys
import tempfile
@@ -17,6 +19,7 @@
from copomus.measures import MinDeltaEnergy, MFECover, Measure
from copomus.mutation import Mutation, parse_mutation_encoding
from copomus.mutation_generators import gen_specific
+from copomus.browser import run as run_browser
class CopomuSTests(unittest.TestCase):
@@ -151,6 +154,42 @@ def test_cli_explicit_mutation_zero_energy_csv(self):
self.assertEqual(row['minDeltaE_min'], '0')
self.assertNotIn('\r', stdout.getvalue())
+ def test_browser_json_runner_reuses_scientific_workflow(self):
+ calls = []
+ energies = iter((-5, -1, -1, -4))
+
+ async def predict(payload):
+ call = json.loads(payload)
+ calls.append(call)
+ energy = next(energies)
+ columns = call['columns']
+ values = {
+ 'id1': 'target', 'start1': 1, 'end1': 2,
+ 'id2': 'query', 'start2': 1, 'end2': 2,
+ 'subseqDP': 'GC&GC', 'hybridDP': '()&()', 'E': energy,
+ }
+ return json.dumps({'csv': ';'.join(columns) + '\n'
+ + ';'.join(str(values[column]) for column in columns) + '\n',
+ 'files': {}})
+
+ progress = []
+ request = {
+ 'query': 'GC', 'target': 'GC', 'qIdxPos0': 1, 'tIdxPos0': 1,
+ 'copomus': {
+ 'measures': ['E'], 'candidateSelection': 'mfe',
+ 'candidateFilters': [], 'generator': 'flip',
+ 'mutationEncoding': 'G1C&C2G', 'alpha': 1, 'beta': 1,
+ },
+ }
+ result = json.loads(asyncio.run(run_browser(json.dumps(request), predict, progress.append)))
+ self.assertEqual(len(calls), 4)
+ self.assertTrue(all(call['query'] and call['target'] for call in calls))
+ self.assertEqual(result['candidates'][0]['values']['mutation'], 'G1C&C2G')
+ self.assertEqual(result['candidates'][0]['values']['E_is_valid'], 1)
+ self.assertEqual(result['candidates'][0]['interactions']['mm']['E'], -4)
+ self.assertTrue(result['tsv'].startswith('mutation\trank\tqIndex\ttIndex'))
+ self.assertIn('Evaluating mutation 1 of 1', progress[-1])
+
if __name__ == '__main__':
unittest.main()
diff --git a/scripts/wasm/build.sh b/scripts/wasm/build.sh
index 10499d68..14268dbe 100644
--- a/scripts/wasm/build.sh
+++ b/scripts/wasm/build.sh
@@ -12,7 +12,7 @@ jobs=${JOBS:-2}
for tool in emcc em++ emar emranlib emconfigure emmake curl pkg-config node python3; do
command -v "$tool" >/dev/null || { echo "Missing tool: $tool" >&2; exit 1; }
done
-mkdir -p "$build/downloads" "$build/sources" "$prefix" "$build/site/wasm"
+mkdir -p "$build/downloads" "$build/sources" "$prefix" "$build/site/wasm" "$build/site/vendor/pyodide"
fetch() {
bash "$repo/scripts/wasm/download.sh" "$1" "$build/downloads/$2" "$3"
}
@@ -20,6 +20,19 @@ fetch https://zlib.net/fossils/zlib-1.3.1.tar.gz zlib-1.3.1.tar.gz \
9a93b2b7dfdac77ceba5a558a580e74667dd6fede4585b91eefb60f03b72df23
fetch https://archives.boost.io/release/1.87.0/source/boost_1_87_0.tar.bz2 boost_1_87_0.tar.bz2 \
af57be25cb4c4f4b413ed692fe378affb4352ea50fbe294a11ef548f4d527d89
+pyodide_version=314.0.7
+fetch "https://registry.npmjs.org/pyodide/-/pyodide-$pyodide_version.tgz" "pyodide-$pyodide_version.tgz" \
+ 66b7949e5a0cba2250b586d7e368bf12fb482800748d182c4618254b685ffaa0
+fetch "https://raw.githubusercontent.com/pyodide/pyodide/$pyodide_version/LICENSE" pyodide-LICENSE.txt \
+ 1f256ecad192880510e84ad60474eab7589218784b9a50bc7ceee34c2b91f1d5
+pyodide_source="$build/sources/pyodide-$pyodide_version"
+mkdir -p "$pyodide_source"
+if [[ ! -s "$pyodide_source/pyodide.mjs" ]]; then
+ tar -xzf "$build/downloads/pyodide-$pyodide_version.tgz" -C "$pyodide_source" --strip-components=1
+fi
+for file in pyodide.mjs pyodide.asm.mjs pyodide.asm.wasm pyodide-lock.json python_stdlib.zip; do
+ cp "$pyodide_source/$file" "$build/site/vendor/pyodide/$file"
+done
# CI supplies the newest stable 2.x manifest; local builds use the checked-in pin.
read -r vienna_version vienna_url vienna_sha256 < <(
python3 "$repo/scripts/wasm/vienna-release.py" --fields \
@@ -109,5 +122,5 @@ 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 "$repo" status --porcelain --untracked-files=no)" \
- "$vienna_version" "$vienna_url" "$vienna_sha256"
+ "$vienna_version" "$vienna_url" "$vienna_sha256" "$pyodide_version"
echo "WASM assets: $build/site/wasm"
diff --git a/scripts/wasm/stage.sh b/scripts/wasm/stage.sh
index 62b6cb3c..da34865a 100644
--- a/scripts/wasm/stage.sh
+++ b/scripts/wasm/stage.sh
@@ -7,20 +7,22 @@ site="$build/site"
test -s "$site/wasm/intarna.js"
test -s "$site/wasm/intarna.wasm"
# Select notices from the archive used by these assets, including dlib upgrades.
-read -r vienna_version vienna_sha256 dlib_directory < <(python3 - "$site" "$build" <<'PYSOURCE'
+read -r vienna_version vienna_sha256 dlib_directory pyodide_version < <(python3 - "$site" "$build" <<'PYSOURCE'
import json, re, sys
from pathlib import Path
site, build = map(Path, sys.argv[1:])
metadata = json.loads((site / "build-info.json").read_text())
archive = metadata["viennarnaArchive"]
-version, digest = archive["version"], archive["sha256"]
+version, digest, pyodide = archive["version"], archive["sha256"], metadata["pyodide"]
if version != metadata["viennarna"] or not re.fullmatch(r"2\.\d+\.\d+", version) or not re.fullmatch(r"[0-9a-f]{64}", digest):
raise SystemExit("Invalid compiled ViennaRNA archive identity")
+if not re.fullmatch(r"\d+\.\d+\.\d+", pyodide):
+ raise SystemExit("Invalid staged Pyodide version")
source = build / "sources" / f"vienna-{version}-{digest}" / f"ViennaRNA-{version}"
dlib = list((source / "src").glob("dlib-*/dlib/LICENSE.txt"))
if len(dlib) != 1 or not re.fullmatch(r"dlib-[0-9.]+", dlib[0].parent.parent.name):
raise SystemExit("Expected one bundled dlib license in the compiled ViennaRNA source")
-print(version, digest, dlib[0].parent.parent.name)
+print(version, digest, dlib[0].parent.parent.name, pyodide)
PYSOURCE
)
vienna_source="$build/sources/vienna-$vienna_version-$vienna_sha256/ViennaRNA-$vienna_version"
@@ -28,13 +30,20 @@ mkdir -p "$site/licenses"
cp -R "$repo/gui/assets" "$repo/gui/examples" "$repo/gui/vendor" "$site/"
test "$(sha256sum "$repo/gui/vendor/plotly-cartesian.min.js" | cut -d' ' -f1)" = "aaf12ff1d4671f7e93f6df4291651ab4ca6b76c0ea5f1576ec1030e3c2819a20"
test "$(sha256sum "$repo/gui/vendor/plotly.css" | cut -d' ' -f1)" = "3bcf2679b557067d8a3492b74092e946544d1cb8b2a72f278bcba95df59afd33"
-for file in index.html styles.css app.js mark.svg protocol.js runner.js results.js options.js columns.js archive.js sessions.js visualization.js output-visualization.js parameter-file.js uploads.js; do
+for file in index.html styles.css app.js mark.svg protocol.js runner.js results.js options.js columns.js archive.js sessions.js visualization.js output-visualization.js parameter-file.js uploads.js copomus.js copomus-options.js; do
cp "$repo/gui/$file" "$site/$file"
done
cp "$repo/gui/intarna-worker.js" "$site/intarna-worker.js"
+cp "$repo/gui/copomus-worker.js" "$site/copomus-worker.js"
+mkdir -p "$site/python/copomus"
+cp "$repo/python/intarna_tools.py" "$site/python/intarna_tools.py"
+for file in __init__.py browser.py workflow.py IntaRNA.py indexing.py candidate_filters.py measures.py mutation.py mutation_generators.py; do
+ cp "$repo/python/copomus/$file" "$site/python/copomus/$file"
+done
touch "$site/.nojekyll"
cp "$repo/src/bin/nlohmann/LICENSE.MIT" "$site/licenses/nlohmann-json.txt"
cp "$repo/gui/vendor/plotly-LICENSE.txt" "$site/licenses/Plotly.txt"
+cp "$build/downloads/pyodide-LICENSE.txt" "$site/licenses/Pyodide.txt"
cp "$repo/LICENSE" "$site/licenses/IntaRNA.txt"
cp "$repo/src/easylogging++.LICENCE.txt" "$site/licenses/easylogging.txt"
cp "$repo/src/mdspan/LICENSE" "$site/licenses/mdspan.txt"
@@ -53,11 +62,12 @@ cat > "$site/licenses/index.html" <IntaRNA licenses
IntaRNA and third-party notices
IntaRNA: Bioinformatics Group of Prof. Backofen, University of Freiburg.
ViennaRNA: authors and Institute for Theoretical Chemistry, University of Vienna.
-This distribution uses ViennaRNA $vienna_version, Boost 1.87.0, zlib 1.3.1, bundled dlib ${dlib_directory#dlib-}, Plotly.js 4.1.2, Kokkos mdspan, Easylogging++ and the Emscripten 4.0.23 runtime.
+This distribution uses ViennaRNA $vienna_version, Boost 1.87.0, zlib 1.3.1, bundled dlib ${dlib_directory#dlib-}, Plotly.js 4.1.2, Pyodide $pyodide_version, Kokkos mdspan, Easylogging++ and the Emscripten 4.0.23 runtime.
- IntaRNA
- ViennaRNA
- nlohmann/json
- Plotly.js
+- Pyodide
- Boost
- zlib
- dlib
- Naview
- Kokkos mdspan
- Easylogging++
@@ -78,5 +88,8 @@ if not (site / "build-info.txt").is_file():
for name, digest in metadata["sha256"].items():
if hashlib.sha256((site / "wasm" / name).read_bytes()).hexdigest() != digest:
raise SystemExit(f"Mismatched engine: {name}")
+for name, digest in metadata["pyodideSha256"].items():
+ if hashlib.sha256((site / "vendor" / "pyodide" / name).read_bytes()).hexdigest() != digest:
+ raise SystemExit(f"Mismatched Pyodide runtime: {name}")
PYINFO
echo "Static site: $site"
diff --git a/scripts/wasm/test-browser.py b/scripts/wasm/test-browser.py
index 8457c058..aa3f3bc6 100644
--- a/scripts/wasm/test-browser.py
+++ b/scripts/wasm/test-browser.py
@@ -33,7 +33,7 @@ def viewer(route):
status = page.locator('#result-status')
sessions = page.locator('.session')
active = page.locator('.session:has([data-role=panel]:not([hidden]))')
- rows = active.locator('tbody tr')
+ rows = active.locator('[data-role=results-view] tbody tr')
def open_group(key):
page.locator('#tab-' + key).click()
@@ -42,6 +42,12 @@ def open_group(key):
assert page.locator('.parameter-group:visible').count() == 1
def load_reference(task='prediction'):
+ if task == 'evaluation':
+ page.get_by_role('radio', name='Evaluation').check()
+ elif task == 'mutation':
+ page.get_by_role('radio', name='Mutation Design').check()
+ else:
+ page.get_by_role('radio', name='Prediction').check()
page.locator('#examples-menu summary').click()
page.locator(f'#example-options [data-example-task="{task}"]').click()
expect(page.locator('#query')).not_to_have_value('')
@@ -54,10 +60,14 @@ def load_reference(task='prediction'):
page.locator('#reset').click()
if task == 'evaluation':
page.get_by_role('radio', name='Evaluation').check()
+ elif task == 'mutation':
+ page.get_by_role('radio', name='Mutation Design').check()
page.locator('#query').fill('>query\nGGGAGGAGGG\n')
page.locator('#target').fill('>target\nCCCUCCUCCC\n')
if task == 'evaluation':
page.locator('#rri').fill('1||||||||||&1||||||||||')
+ elif task == 'mutation':
+ page.locator('#copomus-mutation-encoding').fill('G1C&C10G')
expect(page.locator('#query')).to_have_value('>query\nGGGAGGAGGG\n')
def download_archive(session=None):
@@ -106,11 +116,18 @@ def predict():
page.locator('#examples-menu summary').click()
prediction_example = page.locator('#example-options [data-example-task="prediction"]')
evaluation_example = page.locator('#example-options [data-example-task="evaluation"]')
+ mutation_example = page.locator('#example-options [data-example-task="mutation"]')
expect(prediction_example).to_be_visible()
expect(evaluation_example).not_to_be_visible()
+ expect(mutation_example).not_to_be_visible()
page.get_by_role('radio', name='Evaluation').check()
expect(evaluation_example).to_be_visible()
expect(prediction_example).not_to_be_visible()
+ expect(mutation_example).not_to_be_visible()
+ page.get_by_role('radio', name='Mutation Design').check()
+ expect(mutation_example).to_be_visible()
+ expect(prediction_example).not_to_be_visible()
+ expect(evaluation_example).not_to_be_visible()
page.get_by_role('radio', name='Prediction').check()
page.locator('#examples-menu summary').click()
@@ -311,7 +328,7 @@ def predict():
page.locator('#outCsvSort').select_option('E')
predict()
expect(rows).to_have_count(10)
- assert active.locator('.table-scroll').evaluate('''node => {
+ assert active.locator('[data-role=results-view] .table-scroll').evaluate('''node => {
const body = node.querySelector('tbody');
const copies = [...body.children].map(row => row.cloneNode(true));
body.append(...copies);
@@ -331,9 +348,9 @@ def predict():
active.locator('[data-role=search]').fill('no match')
expect(active.locator('[data-role=no-matches]')).to_be_visible()
active.locator('[data-role=search]').fill('')
- active.locator('.column-picker summary').click()
+ active.locator('[data-role=results-view] .column-picker summary').click()
active.locator('[data-role=visible-columns] input[value="start1"]').uncheck()
- assert 'Target start' not in active.locator('thead').inner_text()
+ assert 'Target start' not in active.locator('[data-role=results-view] thead').inner_text()
active.locator('[data-role=visible-columns] input[value="start1"]').check()
with page.expect_download() as downloaded:
active.locator('[data-role=download]').click()
@@ -460,7 +477,7 @@ def predict():
predict()
expect(status).to_contain_text('Evaluation complete')
expect(rows).to_have_count(2)
- expect(active.locator('thead')).to_contain_text('ED1')
+ expect(active.locator('[data-role=results-view] thead')).to_contain_text('ED1')
expect(active.locator('[data-role=file-list] summary')).to_contain_text('intarna-detailed.txt')
active.locator('[data-role=file-list] summary').click()
expect(active.locator('[data-role=file-list] pre')).to_contain_text('-21.4')
@@ -521,7 +538,7 @@ def predict():
assert download_archive()['intarna-interactions.csv'].count('\n') == 1
fill('query', '>)
\nGGGAGGAGGG')
predict()
- assert active.locator('tbody img').count() == 0
+ assert active.locator('[data-role=results-view] tbody img').count() == 0
assert ' pathToFileURL(resolve(site, 'wasm/intarna.wasm')).href, print: (line) => lines.push(line), printErr: (line) => lines.push(line) });
@@ -15,11 +16,12 @@ if (match[2] !== viennaVersion) throw new Error(`Compiled ViennaRNA ${match[2]}
const metadata = {
source: 'https://github.com/BackofenLab/IntaRNA', commit,
dirty: !!changes,
- intarna: match[1], viennarna: match[2], boost: match[3], emscripten, zlib: '1.3.1',
+ intarna: match[1], viennarna: match[2], boost: match[3], emscripten, zlib: '1.3.1', pyodide: pyodideVersion,
viennarnaArchive: { version: viennaVersion, url: viennaUrl, sha256: viennaSha256 },
threading: 'single worker per task',
sha256: Object.fromEntries(['intarna.js', 'intarna.wasm'].map((name) => [name, createHash('sha256').update(readFileSync(resolve(site, 'wasm', name))).digest('hex')])),
+ pyodideSha256: Object.fromEntries(['pyodide.mjs', 'pyodide.asm.mjs', 'pyodide.asm.wasm', 'pyodide-lock.json', 'python_stdlib.zip'].map((name) => [name, createHash('sha256').update(readFileSync(resolve(site, 'vendor/pyodide', name))).digest('hex')])),
};
writeFileSync(resolve(site, 'build-info.json'), JSON.stringify(metadata, null, 2) + '\n');
-writeFileSync(resolve(site, 'build-info.txt'), `${version}\nIntaRNA repository: ${metadata.source}\nIntaRNA revision: ${metadata.commit}${metadata.dirty ? ' (modified sources)' : ''}\nEmscripten: ${emscripten}\nzlib: ${metadata.zlib}\nViennaRNA archive: ${viennaUrl}\nViennaRNA archive SHA-256: ${viennaSha256}\n${Object.entries(metadata.sha256).map(([name, hash]) => `SHA-256 ${name}: ${hash}`).join('\n')}\n`);
+writeFileSync(resolve(site, 'build-info.txt'), `${version}\nIntaRNA repository: ${metadata.source}\nIntaRNA revision: ${metadata.commit}${metadata.dirty ? ' (modified sources)' : ''}\nEmscripten: ${emscripten}\nPyodide: ${pyodideVersion}\nzlib: ${metadata.zlib}\nViennaRNA archive: ${viennaUrl}\nViennaRNA archive SHA-256: ${viennaSha256}\n${Object.entries(metadata.sha256).map(([name, hash]) => `SHA-256 ${name}: ${hash}`).join('\n')}\n${Object.entries(metadata.pyodideSha256).map(([name, hash]) => `SHA-256 Pyodide ${name}: ${hash}`).join('\n')}\n`);
console.log(`Recorded compiled versions: IntaRNA ${match[1]}, ViennaRNA ${match[2]}, Boost ${match[3]}`);