diff --git a/.github/dependabot.yml b/.github/dependabot.yml index 9fd8c31f1..9f94a8874 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -6,6 +6,8 @@ updates: interval: weekly commit-message: prefix: "chore(github-actions)" + cooldown: + default-days: 7 - package-ecosystem: npm directory: website/ schedule: @@ -16,6 +18,8 @@ updates: commit-message: prefix: "chore(website)" target-branch: "main" + cooldown: + default-days: 7 - package-ecosystem: npm directory: website/ schedule: @@ -27,6 +31,8 @@ updates: - "patch" commit-message: prefix: "chore(website)" + cooldown: + default-days: 7 - package-ecosystem: gradle directory: backend/ schedule: @@ -38,3 +44,5 @@ updates: - "patch" commit-message: prefix: "chore(backend)" + cooldown: + default-days: 7 diff --git a/.github/workflows/e2e.yml b/.github/workflows/e2e.yml index 5eb1736cd..1f67161c1 100644 --- a/.github/workflows/e2e.yml +++ b/.github/workflows/e2e.yml @@ -70,6 +70,22 @@ jobs: env: BACKEND_URL: http://localhost:9021 + - name: Collect container logs + if: ${{ always() && !cancelled() }} + run: | + mkdir -p /tmp/container-logs + services="$(docker compose -f ../docker-compose.yml config --services || true)" + for service in $services; do + docker compose -f ../docker-compose.yml logs --no-color "$service" > "/tmp/container-logs/${service}.log" || true + done + + - uses: actions/upload-artifact@v7 + if: ${{ always() && !cancelled() }} + with: + name: container-logs + path: /tmp/container-logs/ + retention-days: 7 + - uses: actions/upload-artifact@v7 if: ${{ !cancelled() }} with: diff --git a/.github/workflows/rebaseProd.yml b/.github/workflows/rebaseProd.yml index 7b2cff63b..8ce6f792f 100644 --- a/.github/workflows/rebaseProd.yml +++ b/.github/workflows/rebaseProd.yml @@ -26,9 +26,9 @@ jobs: echo "PR to update prod from main already exists - skipping creation" else body="This pull request updates the \`prod\` branch with the latest changes from the \`main\` branch. - - ### Make sure to merge this creating a merge commit. - **Do not squash-merge** this PR. **Do not rebase and merge**." - + + # ⚠️ Do not squash-merge! ⚠️ + Make sure to merge this creating a merge commit." + gh pr create --base prod --head main --title "chore: update prod from main" --body "$body" fi diff --git a/collection-seeding/README.md b/collection-seeding/README.md index 3ed909a5f..5a6a7d853 100644 --- a/collection-seeding/README.md +++ b/collection-seeding/README.md @@ -5,6 +5,8 @@ Seeds the backend with example collections: - **covid-resistance-mutations** — resistance mutation data for 3CLpro, RdRp, and Spike mAb - **covid-pango-lineages** — one collection per pango lineage, with nucleotide substitutions as variants - **covid-pango-lineages-sample** — same as above but limited to 10 lineages, for quick testing +- **rsv-a-resistance-mutations** — RSV-A F protein resistance mutations against Nirsevimab and Palivizumab (fetched live from ViralZone) +- **rsv-b-resistance-mutations** — RSV-B F protein resistance mutations against Nirsevimab and Palivizumab (fetched live from ViralZone) The script is idempotent — re-running it will create new collections or update existing ones (matched by name). If a collection's name changes in the source, the old entry is orphaned and a new one is created. @@ -30,11 +32,18 @@ Then use the provided tasks: ```bash pixi run seed # all sources -pixi run seed-resistance # resistance mutations only +pixi run seed-resistance # COVID resistance mutations only pixi run seed-lineages # pango lineages only pixi run seed-lineages-sample # first 10 pango lineages (quick test) ``` +RSV sources don't have dedicated tasks — use `--source` directly: + +```bash +pixi run seed --source rsv-a-resistance-mutations +pixi run seed --source rsv-b-resistance-mutations +``` + To target a different backend: ```bash diff --git a/collection-seeding/sources/pango_lineages.py b/collection-seeding/sources/covid_pango_lineages.py similarity index 93% rename from collection-seeding/sources/pango_lineages.py rename to collection-seeding/sources/covid_pango_lineages.py index 048d89b64..78ccbd7d1 100644 --- a/collection-seeding/sources/pango_lineages.py +++ b/collection-seeding/sources/covid_pango_lineages.py @@ -9,7 +9,7 @@ ) -class PangoLineagesSource(Source): +class CovidPangoLineagesSource(Source): """Source: Pango lineage definitions from corneliusroemer/pango-sequences. Creates one collection per lineage, with nucleotide substitutions as variants. @@ -82,8 +82,8 @@ def _build_collection(self, entry: dict) -> Collection: } -class PangoLineagesSampleSource(PangoLineagesSource): - """Same as PangoLineagesSource but limited to the first 10 lineages, for quick testing.""" +class CovidPangoLineagesSampleSource(CovidPangoLineagesSource): + """Same as CovidPangoLineagesSource but limited to the first 10 lineages, for quick testing.""" name = "covid-pango-lineages-sample" include_in_default_run = False diff --git a/collection-seeding/sources/resistance_mutations.py b/collection-seeding/sources/covid_resistance_mutations.py similarity index 99% rename from collection-seeding/sources/resistance_mutations.py rename to collection-seeding/sources/covid_resistance_mutations.py index 30ca66501..0f656043b 100644 --- a/collection-seeding/sources/resistance_mutations.py +++ b/collection-seeding/sources/covid_resistance_mutations.py @@ -2,7 +2,7 @@ from sources import Source -class ResistanceMutationsSource(Source): +class CovidResistanceMutationsSource(Source): """Source: SARS-CoV-2 antiviral resistance mutations (ported from seed.mjs). Three collections covering 3CLpro, RdRp, and Spike mAb resistance mutations diff --git a/collection-seeding/sources/registry.py b/collection-seeding/sources/registry.py index 88d704005..d3915a1d8 100644 --- a/collection-seeding/sources/registry.py +++ b/collection-seeding/sources/registry.py @@ -4,12 +4,15 @@ place that needs to change — seed.py discovers sources exclusively through this list. """ -from sources.pango_lineages import PangoLineagesSource, PangoLineagesSampleSource -from sources.resistance_mutations import ResistanceMutationsSource +from sources.covid_pango_lineages import CovidPangoLineagesSource, CovidPangoLineagesSampleSource +from sources.covid_resistance_mutations import CovidResistanceMutationsSource +from sources.rsv_resistance_mutations import RsvAResistanceMutationsSource, RsvBResistanceMutationsSource from sources import Source ALL_SOURCES: list[type[Source]] = [ - ResistanceMutationsSource, - PangoLineagesSource, - PangoLineagesSampleSource, + CovidResistanceMutationsSource, + RsvAResistanceMutationsSource, + RsvBResistanceMutationsSource, + CovidPangoLineagesSource, + CovidPangoLineagesSampleSource, ] diff --git a/collection-seeding/sources/rsv_resistance_mutations.py b/collection-seeding/sources/rsv_resistance_mutations.py new file mode 100644 index 000000000..e84518e5f --- /dev/null +++ b/collection-seeding/sources/rsv_resistance_mutations.py @@ -0,0 +1,81 @@ +import re +import requests + +from models import Collection, Variant +from sources import Source + +DATA_URL = "https://viralzone.expasy.org/resources/RSV/F_RSV_human.txt" + +# Regex for row parsing. The file is a TSV file, but sometimes also uses spaces. +# Columns 1 (A/B) and 2 (mutation) never contain spaces; column 3 (comment) may. +_ROW_RE = re.compile(r"^\s*([AB])\s+(\S+)\s+(.+)") + + +def _fetch_rows() -> list[tuple[str, list[str], str, str]]: + response = requests.get(DATA_URL, timeout=60) + response.raise_for_status() + return _parse_rows(response.text) + + +def _parse_rows(text: str) -> list[tuple[str, list[str], str, str]]: + """Parse ViralZone RSV resistance text into (rsv_type, aa_mutations, antibody, resistance_type) tuples.""" + rows = [] + for line in text.splitlines(): + m = _ROW_RE.match(line) + if not m: + continue + rsv_type, aa_str, comment = m.group(1), m.group(2), m.group(3).strip() + aa_mutations = [f"F:{part}" for part in aa_str.split("+")] + if "Nirsevimab" in comment: + antibody = "Nirsevimab" + elif "Palivizumab" in comment: + antibody = "Palivizumab" + else: + continue + resistance_type = "Partial resistance" if "Partial resistance" in comment else "Resistance" + rows.append((rsv_type, aa_mutations, antibody, resistance_type)) + return rows + + +def _build_collections(rsv_type: str, organism: str, owned_tag: str) -> list[Collection]: + all_rows = _fetch_rows() + type_rows = [(aa, ab, res) for (t, aa, ab, res) in all_rows if t == rsv_type] + collections = [] + for antibody in ("Nirsevimab", "Palivizumab"): + variants: list[Variant] = [ + { + "type": "filterObject", + "name": res_type, + "filterObject": {"aminoAcidMutations": aa}, + } + for (aa, ab, res_type) in type_rows + if ab == antibody + ] + collections.append({ + "name": f"{antibody} resistance mutations", + "organism": organism, + "description": ( + f"RSV F protein resistance mutations against {antibody} " + f"as per ViralZone (https://viralzone.expasy.org/11605). {owned_tag}" + ), + "variants": variants, + }) + return collections + + +class RsvAResistanceMutationsSource(Source): + name = "rsv-a-resistance-mutations" + organism = "rsvA" + owned_tag = "#resistance-mutation" + + def get_collections(self) -> list[Collection]: + return _build_collections("A", self.organism, self.owned_tag) + + +class RsvBResistanceMutationsSource(Source): + name = "rsv-b-resistance-mutations" + organism = "rsvB" + owned_tag = "#resistance-mutation" + + def get_collections(self) -> list[Collection]: + return _build_collections("B", self.organism, self.owned_tag) diff --git a/collection-seeding/tests/test_pango_lineages.py b/collection-seeding/tests/test_pango_lineages.py index 057301e30..420e306e6 100644 --- a/collection-seeding/tests/test_pango_lineages.py +++ b/collection-seeding/tests/test_pango_lineages.py @@ -1,6 +1,6 @@ import responses as rsps_lib -from sources.pango_lineages import PangoLineagesSource, DATA_URL +from sources.covid_pango_lineages import CovidPangoLineagesSource, DATA_URL SAMPLE_DATA = { "BA.2": { @@ -40,20 +40,20 @@ def test_name(): - assert PangoLineagesSource.name == "covid-pango-lineages" + assert CovidPangoLineagesSource.name == "covid-pango-lineages" # --- _build_collection --- def test_build_collection_basic(): - col = PangoLineagesSource()._build_collection(SAMPLE_DATA["BA.2"]) + col = CovidPangoLineagesSource()._build_collection(SAMPLE_DATA["BA.2"]) assert col["name"] == "BA.2" assert col["organism"] == "covid" def test_build_collection_description_format(): - col = PangoLineagesSource()._build_collection(SAMPLE_DATA["BA.2"]) + col = CovidPangoLineagesSource()._build_collection(SAMPLE_DATA["BA.2"]) assert "BA.2" in col["description"] assert "BA" in col["description"] # parent assert "22C" in col["description"] # clade @@ -61,18 +61,18 @@ def test_build_collection_description_format(): def test_build_collection_missing_fields_use_defaults(): - col = PangoLineagesSource()._build_collection(SAMPLE_DATA["XBB"]) + col = CovidPangoLineagesSource()._build_collection(SAMPLE_DATA["XBB"]) assert "—" in col["description"] # parent and clade fallback assert "unknown" in col["description"] # date fallback def test_build_collection_always_four_variants(): - col = PangoLineagesSource()._build_collection(SAMPLE_DATA["BA.2"]) + col = CovidPangoLineagesSource()._build_collection(SAMPLE_DATA["BA.2"]) assert len(col["variants"]) == 4 def test_build_collection_variant_names(): - col = PangoLineagesSource()._build_collection(SAMPLE_DATA["BA.2"]) + col = CovidPangoLineagesSource()._build_collection(SAMPLE_DATA["BA.2"]) names = [v["name"] for v in col["variants"]] assert names == [ "Nucleotide substitutions", @@ -83,7 +83,7 @@ def test_build_collection_variant_names(): def test_build_collection_variant_filter_keys(): - col = PangoLineagesSource()._build_collection(SAMPLE_DATA["BA.2"]) + col = CovidPangoLineagesSource()._build_collection(SAMPLE_DATA["BA.2"]) variants = col["variants"] assert "nucleotideMutations" in variants[0]["filterObject"] assert "aminoAcidMutations" in variants[1]["filterObject"] @@ -92,7 +92,7 @@ def test_build_collection_variant_filter_keys(): def test_build_collection_variant_contents(): - col = PangoLineagesSource()._build_collection(SAMPLE_DATA["BA.2"]) + col = CovidPangoLineagesSource()._build_collection(SAMPLE_DATA["BA.2"]) variants = col["variants"] assert variants[0]["filterObject"]["nucleotideMutations"] == ["C241T", "A23403G"] assert variants[1]["filterObject"]["aminoAcidMutations"] == ["S:N501Y"] @@ -101,7 +101,7 @@ def test_build_collection_variant_contents(): def test_build_collection_filters_blank_subs(): - col = PangoLineagesSource()._build_collection(SAMPLE_DATA["BA.2"]) + col = CovidPangoLineagesSource()._build_collection(SAMPLE_DATA["BA.2"]) # nucSubstitutions has ["C241T", "A23403G", ""] — blank should be dropped nuc = col["variants"][0]["filterObject"]["nucleotideMutations"] assert "" not in nuc @@ -109,7 +109,7 @@ def test_build_collection_filters_blank_subs(): def test_build_collection_empty_lists_when_all_blanks(): - col = PangoLineagesSource()._build_collection(SAMPLE_DATA["XBB"]) + col = CovidPangoLineagesSource()._build_collection(SAMPLE_DATA["XBB"]) assert len(col["variants"]) == 4 for v in col["variants"]: lists = list(v["filterObject"].values()) @@ -122,7 +122,7 @@ def test_build_collection_empty_lists_when_all_blanks(): @rsps_lib.activate def test_get_collections_fetches_data_url(): rsps_lib.add(rsps_lib.GET, DATA_URL, json=SAMPLE_DATA, status=200) - PangoLineagesSource().get_collections() + CovidPangoLineagesSource().get_collections() assert len(rsps_lib.calls) == 1 assert rsps_lib.calls[0].request.url == DATA_URL @@ -130,7 +130,7 @@ def test_get_collections_fetches_data_url(): @rsps_lib.activate def test_get_collections_includes_all_lineages(): rsps_lib.add(rsps_lib.GET, DATA_URL, json=SAMPLE_DATA, status=200) - cols = PangoLineagesSource().get_collections() + cols = CovidPangoLineagesSource().get_collections() # All lineages included regardless of empty subs names = [c["name"] for c in cols] assert "BA.2" in names @@ -141,12 +141,12 @@ def test_get_collections_includes_all_lineages(): @rsps_lib.activate def test_get_collections_respects_limit(): rsps_lib.add(rsps_lib.GET, DATA_URL, json=SAMPLE_DATA, status=200) - cols = PangoLineagesSource(limit=1).get_collections() + cols = CovidPangoLineagesSource(limit=1).get_collections() assert len(cols) <= 1 @rsps_lib.activate def test_get_collections_no_limit_returns_all(): rsps_lib.add(rsps_lib.GET, DATA_URL, json=SAMPLE_DATA, status=200) - cols = PangoLineagesSource().get_collections() + cols = CovidPangoLineagesSource().get_collections() assert len(cols) == 3 diff --git a/collection-seeding/tests/test_resistance_mutations.py b/collection-seeding/tests/test_resistance_mutations.py index c708f7673..382ede697 100644 --- a/collection-seeding/tests/test_resistance_mutations.py +++ b/collection-seeding/tests/test_resistance_mutations.py @@ -1,8 +1,8 @@ -from sources.resistance_mutations import ResistanceMutationsSource, _mature_name +from sources.covid_resistance_mutations import CovidResistanceMutationsSource, _mature_name def test_name(): - assert ResistanceMutationsSource.name == "covid-resistance-mutations" + assert CovidResistanceMutationsSource.name == "covid-resistance-mutations" # --- _mature_name --- @@ -31,17 +31,17 @@ def test_mature_name_deletion(): def test_get_collections_returns_three(): - cols = ResistanceMutationsSource().get_collections() + cols = CovidResistanceMutationsSource().get_collections() assert len(cols) == 3 def test_get_collections_all_covid(): - for col in ResistanceMutationsSource().get_collections(): + for col in CovidResistanceMutationsSource().get_collections(): assert col["organism"] == "covid" def test_get_collections_variant_structure(): - for col in ResistanceMutationsSource().get_collections(): + for col in CovidResistanceMutationsSource().get_collections(): assert col["variants"], f"'{col['name']}' has no variants" for v in col["variants"]: assert v["type"] == "filterObject" diff --git a/collection-seeding/tests/test_rsv_resistance_mutations.py b/collection-seeding/tests/test_rsv_resistance_mutations.py new file mode 100644 index 000000000..d0b0ffe16 --- /dev/null +++ b/collection-seeding/tests/test_rsv_resistance_mutations.py @@ -0,0 +1,155 @@ +import responses as rsps_lib + +from sources.rsv_resistance_mutations import ( + DATA_URL, + RsvAResistanceMutationsSource, + RsvBResistanceMutationsSource, + _parse_rows, +) + +SAMPLE_TEXT = ( + "#Last update\t14.11.25\n" + "Type\tAA\t\tComment\n" + "\n" + "A\tN67I+N208Y\tNirsevimab Resistance\n" + "A K68E Nirsevimab Partial resistance\t\t\n" + "A\tK272M\t\tPalivizumab Resistance\n" + "B\tI64T\t\tNirsevimab Resistance\t\t\n" + "B\tK65Q\t\tNirsevimab Partial resistance\n" + "B\tK272Q\t\tPalivizumab Resistance\t\n" +) + + +# --- _parse_rows --- + + +def test_parse_rows_single_mutation(): + rows = _parse_rows("B\tI64T\t\tNirsevimab Resistance") + assert rows == [("B", ["F:I64T"], "Nirsevimab", "Resistance")] + + +def test_parse_rows_combo_mutation(): + rows = _parse_rows("A\tN67I+N208Y\tNirsevimab Resistance") + assert rows == [("A", ["F:N67I", "F:N208Y"], "Nirsevimab", "Resistance")] + + +def test_parse_rows_partial_resistance(): + rows = _parse_rows("A\tK68E\t\tNirsevimab Partial resistance") + assert rows[0][3] == "Partial resistance" + + +def test_parse_rows_palivizumab(): + rows = _parse_rows("A\tK272M\t\tPalivizumab Resistance") + assert rows[0][2] == "Palivizumab" + + +def test_parse_rows_with_spaces(): + rows = _parse_rows("A K272M Palivizumab Resistance") + assert rows[0][2] == "Palivizumab" + + +def test_parse_rows_skips_comment_lines(): + rows = _parse_rows(SAMPLE_TEXT) + assert all(r[0] in ("A", "B") for r in rows) + + +def test_parse_rows_skips_header_and_blank_lines(): + rows = _parse_rows(SAMPLE_TEXT) + assert len(rows) == 6 + + +# --- source names --- + + +def test_rsv_a_source_name(): + assert RsvAResistanceMutationsSource.name == "rsv-a-resistance-mutations" + + +def test_rsv_b_source_name(): + assert RsvBResistanceMutationsSource.name == "rsv-b-resistance-mutations" + + +# --- get_collections --- + + +@rsps_lib.activate +def test_rsv_a_returns_two_collections(): + rsps_lib.add(rsps_lib.GET, DATA_URL, body=SAMPLE_TEXT, status=200) + cols = RsvAResistanceMutationsSource().get_collections() + assert len(cols) == 2 + + +@rsps_lib.activate +def test_rsv_a_organism(): + rsps_lib.add(rsps_lib.GET, DATA_URL, body=SAMPLE_TEXT, status=200) + cols = RsvAResistanceMutationsSource().get_collections() + assert all(c["organism"] == "rsvA" for c in cols) + + +@rsps_lib.activate +def test_rsv_b_returns_two_collections(): + rsps_lib.add(rsps_lib.GET, DATA_URL, body=SAMPLE_TEXT, status=200) + cols = RsvBResistanceMutationsSource().get_collections() + assert len(cols) == 2 + + +@rsps_lib.activate +def test_rsv_b_organism(): + rsps_lib.add(rsps_lib.GET, DATA_URL, body=SAMPLE_TEXT, status=200) + cols = RsvBResistanceMutationsSource().get_collections() + assert all(c["organism"] == "rsvB" for c in cols) + + +@rsps_lib.activate +def test_collection_names_are_nirsevimab_and_palivizumab(): + rsps_lib.add(rsps_lib.GET, DATA_URL, body=SAMPLE_TEXT, status=200) + cols = RsvAResistanceMutationsSource().get_collections() + names = {c["name"] for c in cols} + assert names == {"Nirsevimab resistance mutations", "Palivizumab resistance mutations"} + + +@rsps_lib.activate +def test_variant_names_are_resistance_types(): + rsps_lib.add(rsps_lib.GET, DATA_URL, body=SAMPLE_TEXT, status=200) + cols = RsvAResistanceMutationsSource().get_collections() + for col in cols: + for v in col["variants"]: + assert v["name"] in ("Resistance", "Partial resistance") + + +@rsps_lib.activate +def test_variants_have_amino_acid_mutations(): + rsps_lib.add(rsps_lib.GET, DATA_URL, body=SAMPLE_TEXT, status=200) + cols = RsvBResistanceMutationsSource().get_collections() + for col in cols: + for v in col["variants"]: + assert "aminoAcidMutations" in v["filterObject"] + assert len(v["filterObject"]["aminoAcidMutations"]) >= 1 + + +@rsps_lib.activate +def test_combo_mutation_produces_multiple_aa_entries(): + rsps_lib.add(rsps_lib.GET, DATA_URL, body=SAMPLE_TEXT, status=200) + cols = RsvAResistanceMutationsSource().get_collections() + nirsevimab_col = next(c for c in cols if "Nirsevimab" in c["name"]) + combo_variant = next( + v for v in nirsevimab_col["variants"] + if len(v["filterObject"]["aminoAcidMutations"]) > 1 + ) + assert combo_variant["filterObject"]["aminoAcidMutations"] == ["F:N67I", "F:N208Y"] + + +@rsps_lib.activate +def test_only_rsv_b_rows_in_rsv_b_collections(): + rsps_lib.add(rsps_lib.GET, DATA_URL, body=SAMPLE_TEXT, status=200) + cols = RsvBResistanceMutationsSource().get_collections() + # RSV-B Nirsevimab should have I64T and K65Q (not A's K68E) + nirsevimab_col = next(c for c in cols if "Nirsevimab" in c["name"]) + all_aa = [ + aa + for v in nirsevimab_col["variants"] + for aa in v["filterObject"]["aminoAcidMutations"] + ] + assert "F:I64T" in all_aa + assert "F:K65Q" in all_aa + assert "F:K68E" not in all_aa # RSV-A only diff --git a/website/package-lock.json b/website/package-lock.json index 51e83bdfd..9db2ea4ba 100644 --- a/website/package-lock.json +++ b/website/package-lock.json @@ -10,16 +10,17 @@ "dependencies": { "@astrojs/node": "^9.5.3", "@genspectrum/dashboard-components": "^1.17.0", - "@tanstack/react-query": "^5.100.10", + "@tanstack/react-query": "^5.101.0", "astro": "^5.18.1", - "axios": "^1.16.0", - "better-auth": "^1.6.9", + "axios": "^1.16.1", + "better-auth": "^1.6.14", "cookie": "^1.1.1", - "dayjs": "^1.11.20", - "katex": "^0.16.45", + "dayjs": "^1.11.21", + "downshift": "^9.3.3", + "katex": "^0.17.0", "patch-package": "^8.0.1", - "react": "^19.2.6", - "react-dom": "^19.2.6", + "react": "^19.2.7", + "react-dom": "^19.2.7", "react-katex": "^3.1.0", "react-toastify": "^11.1.0", "uuid": "^14.0.0", @@ -36,21 +37,21 @@ "@iconify/tailwind4": "^1.2.3", "@playwright/test": "^1.60.0", "@tailwindcss/vite": "^4.3.0", - "@tanstack/eslint-plugin-query": "^5.100.10", + "@tanstack/eslint-plugin-query": "^5.101.0", "@testing-library/dom": "^10.4.1", "@testing-library/jest-dom": "^6.9.1", "@testing-library/react": "^16.3.2", "@testing-library/user-event": "^14.6.1", - "@types/node": "^24.5.2", - "@types/react": "^19.0.0", + "@types/node": "^24.12.4", + "@types/react": "^19.2.16", "@types/react-dom": "^19.0.0", "@types/react-katex": "^3.0.4", "@types/topojson-specification": "^1.0.5", - "@typescript-eslint/eslint-plugin": "^8.59.3", - "@typescript-eslint/parser": "^8.59.3", + "@typescript-eslint/eslint-plugin": "^8.60.1", + "@typescript-eslint/parser": "^8.60.1", "@vitest/browser": "^3.2.4", "astro-eslint-parser": "^1.4.0", - "daisyui": "^5.5.19", + "daisyui": "^5.5.20", "dotenv": "^16.5.0", "eslint": "^9.39.2", "eslint-plugin-astro": "^1.7.0", @@ -64,7 +65,7 @@ "prettier-plugin-tailwindcss": "^0.8.0", "tailwindcss": "^4.0.9", "typescript": "^5.9.3", - "typescript-eslint": "^8.59.3", + 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true, + "devOptional": true, "license": "MIT", "engines": { "node": ">=10.0.0" @@ -14499,7 +14502,7 @@ "version": "5.0.8", "resolved": "https://registry.npmjs.org/y18n/-/y18n-5.0.8.tgz", "integrity": "sha512-0pfFzegeDWJHJIAmTLRP2DwHjdF5s7jo9tuztdQxAhINCdvS+3nGINqPd00AphqJR/0LhANUS6/+7SCb98YOfA==", - "dev": true, + "devOptional": true, "license": "ISC", "engines": { "node": ">=10" @@ -14556,7 +14559,6 @@ "integrity": "sha512-Thbli+OlOj+iMPYFBVBfJ3OmCAnaSyNn4M1vz9T6Gka5Jt9ba/HIR56joy65tY6kx/FCF5VXNB819Y7/GUrBGA==", "dev": true, "license": "MIT", - "peer": true, "dependencies": { "fast-deep-equal": "^3.1.3", "fast-uri": "^3.0.1", @@ -14614,7 +14616,7 @@ "version": "17.7.2", "resolved": "https://registry.npmjs.org/yargs/-/yargs-17.7.2.tgz", "integrity": "sha512-7dSzzRQ++CKnNI/krKnYRV7JKKPUXMEh61soaHKg9mrWEhzFWhFnxPxGl+69cD1Ou63C13NUPCnmIcrvqCuM6w==", - "dev": true, + "devOptional": true, "license": "MIT", "dependencies": { "cliui": "^8.0.1", @@ -14642,14 +14644,14 @@ "version": "8.0.0", "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-8.0.0.tgz", "integrity": "sha512-MSjYzcWNOA0ewAHpz0MxpYFvwg6yjy1NG3xteoqz644VCo/RPgnr1/GGt+ic3iJTzQ8Eu3TdM14SawnVUmGE6A==", - "dev": true, + "devOptional": true, "license": "MIT" }, "node_modules/yargs/node_modules/string-width": { "version": "4.2.3", "resolved": "https://registry.npmjs.org/string-width/-/string-width-4.2.3.tgz", "integrity": "sha512-wKyQRQpjJ0sIp62ErSZdGsjMJWsap5oRNihHhu6G7JVO/9jIB6UyevL+tXuOqrng8j/cxKTWyWUwvSTriiZz/g==", - "dev": true, + "devOptional": true, "license": "MIT", "dependencies": { "emoji-regex": "^8.0.0", @@ -14664,7 +14666,7 @@ "version": "6.0.1", "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.1.tgz", "integrity": "sha512-Y38VPSHcqkFrCpFnQ9vuSXmquuv5oXOKpGeT6aGrr3o3Gc9AlVa6JBfUSOCnbxGGZF+/0ooI7KrPuUSztUdU5A==", - "dev": true, + "devOptional": true, "license": "MIT", "dependencies": { "ansi-regex": "^5.0.1" @@ -14717,7 +14719,6 @@ "resolved": "https://registry.npmjs.org/zod/-/zod-3.25.76.tgz", "integrity": "sha512-gzUt/qt81nXsFGKIFcC3YnfEAx5NkunCfnDlvuBSSFS02bcXu4Lmea0AFIUwbLWxWPx3d9p8S5QoaujKcNQxcQ==", "license": "MIT", - "peer": true, "funding": { "url": "https://github.com/sponsors/colinhacks" } diff --git a/website/package.json b/website/package.json index ab76c1d72..8a0a94ab2 100644 --- a/website/package.json +++ b/website/package.json @@ -26,16 +26,17 @@ "dependencies": { "@astrojs/node": "^9.5.3", "@genspectrum/dashboard-components": "^1.17.0", - "@tanstack/react-query": "^5.100.10", + "@tanstack/react-query": "^5.101.0", "astro": "^5.18.1", - "axios": "^1.16.0", - "better-auth": "^1.6.9", + "axios": "^1.16.1", + "better-auth": "^1.6.14", "cookie": "^1.1.1", - "dayjs": "^1.11.20", - "katex": "^0.16.45", + "dayjs": "^1.11.21", + "katex": "^0.17.0", + "downshift": "^9.3.3", "patch-package": "^8.0.1", - "react": "^19.2.6", - "react-dom": "^19.2.6", + "react": "^19.2.7", + "react-dom": "^19.2.7", "react-katex": "^3.1.0", "react-toastify": "^11.1.0", "uuid": "^14.0.0", @@ -52,21 +53,21 @@ "@iconify/tailwind4": "^1.2.3", "@playwright/test": "^1.60.0", "@tailwindcss/vite": "^4.3.0", - "@tanstack/eslint-plugin-query": "^5.100.10", + "@tanstack/eslint-plugin-query": "^5.101.0", "@testing-library/dom": "^10.4.1", "@testing-library/jest-dom": "^6.9.1", "@testing-library/react": "^16.3.2", "@testing-library/user-event": "^14.6.1", - "@types/node": "^24.5.2", - "@types/react": "^19.0.0", + "@types/node": "^24.12.4", + "@types/react": "^19.2.16", "@types/react-dom": "^19.0.0", "@types/react-katex": "^3.0.4", "@types/topojson-specification": "^1.0.5", - "@typescript-eslint/eslint-plugin": "^8.59.3", - "@typescript-eslint/parser": "^8.59.3", + "@typescript-eslint/eslint-plugin": "^8.60.1", + "@typescript-eslint/parser": "^8.60.1", "@vitest/browser": "^3.2.4", "astro-eslint-parser": "^1.4.0", - "daisyui": "^5.5.19", + "daisyui": "^5.5.20", "dotenv": "^16.5.0", "eslint": "^9.39.2", "eslint-plugin-astro": "^1.7.0", @@ -80,7 +81,7 @@ "prettier-plugin-tailwindcss": "^0.8.0", "tailwindcss": "^4.0.9", "typescript": "^5.9.3", - "typescript-eslint": "^8.59.3", + "typescript-eslint": "^8.60.1", "vitest": "^3.2.4", "vitest-browser-react": "^1.0.1", "zod": "^3.25.74" diff --git a/website/src/backendApi/backendService.ts b/website/src/backendApi/backendService.ts index 8019e6d9d..dbe332519 100644 --- a/website/src/backendApi/backendService.ts +++ b/website/src/backendApi/backendService.ts @@ -177,8 +177,21 @@ export class BackendService extends ApiService { return this.get({ url: `/users/${id}`, schema: publicUserSchema }); } - public async getCollectionSummaries(requestParams: { organism?: string; excludeSystemCollections?: boolean } = {}) { - return this.get({ url: '/collections', requestParams, schema: z.array(collectionSummarySchema) }); + public async getCollectionSummaries({ + organism, + userId, + excludeSystemCollections, + }: { organism?: string; userId?: number; excludeSystemCollections?: boolean } = {}) { + const requestParams: Record = {}; + if (organism !== undefined) requestParams.organism = organism; + if (userId !== undefined) requestParams.userId = String(userId); + if (excludeSystemCollections !== undefined) + requestParams.excludeSystemCollections = String(excludeSystemCollections); + return this.get({ + url: '/collections', + requestParams: Object.keys(requestParams).length > 0 ? requestParams : undefined, + schema: z.array(collectionSummarySchema), + }); } public async getCollections({ organism }: { organism?: string } = {}) { diff --git a/website/src/components/pageStateSelectors/wasap/InfoBlocks.tsx b/website/src/components/pageStateSelectors/wasap/InfoBlocks.tsx index c75b1b337..715d4940f 100644 --- a/website/src/components/pageStateSelectors/wasap/InfoBlocks.tsx +++ b/website/src/components/pageStateSelectors/wasap/InfoBlocks.tsx @@ -144,12 +144,12 @@ export function ExplorationModeInfo() {
  • Variant Explorer: track variant-specific - mutations over time. Variant-specific mutations are computed based on user parameters and filtering - clinical sequences from{' '} + mutations over time. Variants can be defined in two ways: by selecting a predefined variant from a + curated list, or by filtering clinical sequences from{' '} CovSpectrum - - . + {' '} + based on user parameters.
  • Untracked Mutations: novel mutations not yet diff --git a/website/src/components/pageStateSelectors/wasap/WasapPageStateSelector.tsx b/website/src/components/pageStateSelectors/wasap/WasapPageStateSelector.tsx index 5f5c483ff..f968b786d 100644 --- a/website/src/components/pageStateSelectors/wasap/WasapPageStateSelector.tsx +++ b/website/src/components/pageStateSelectors/wasap/WasapPageStateSelector.tsx @@ -1,6 +1,7 @@ import { useQuery } from '@tanstack/react-query'; import { type Dispatch, type SetStateAction, useState } from 'react'; +import { getBackendServiceForClientside } from '../../../backendApi/backendService'; import { ApplyFilterButton } from '../ApplyFilterButton'; import { DynamicDateFilter } from '../DynamicDateFilter'; import { SelectorHeadline } from '../SelectorHeadline'; @@ -101,6 +102,24 @@ export function WasapPageStateSelector({ }, }); + const predefinedVariantsQueryResult = useQuery({ + enabled: config.variantAnalysisModeEnabled && config.predefinedVariantsSource !== undefined, + queryKey: ['predefinedVariants', config.variantAnalysisModeEnabled && config.predefinedVariantsSource], + queryFn: async () => { + if (!config.variantAnalysisModeEnabled || config.predefinedVariantsSource === undefined) { + throw Error( + 'This predefined variants query was called despite it being disabled. This should not happen.', + ); + } + const { collectionsUserId, collectionsTag } = config.predefinedVariantsSource; + const collections = await getBackendServiceForClientside().getCollectionSummaries({ + userId: collectionsUserId, + organism: config.internalName, + }); + return collections.filter((c) => c.description?.includes(collectionsTag) ?? false); + }, + }); + return (
    Filter dataset @@ -181,6 +200,12 @@ export function WasapPageStateSelector({ setPageState={setVariantFilter} clinicalSequenceLapisBaseUrl={config.clinicalLapis.lapisBaseUrl} clinicalSequenceLapisLineageField={config.clinicalLapis.lineageField} + predefinedVariantsQueryResult={ + config.predefinedVariantsSource !== undefined + ? predefinedVariantsQueryResult + : undefined + } + predefinedVariantsLabel={config.predefinedVariantsSource?.variantSourceLabel} /> ); case 'resistance': diff --git a/website/src/components/pageStateSelectors/wasap/filters/VariantExplorerFilter.browser.spec.tsx b/website/src/components/pageStateSelectors/wasap/filters/VariantExplorerFilter.browser.spec.tsx index dca132918..e3c3e69ff 100644 --- a/website/src/components/pageStateSelectors/wasap/filters/VariantExplorerFilter.browser.spec.tsx +++ b/website/src/components/pageStateSelectors/wasap/filters/VariantExplorerFilter.browser.spec.tsx @@ -1,17 +1,26 @@ -import { userEvent } from '@vitest/browser/context'; +import { type UseQueryResult } from '@tanstack/react-query'; +import { page, userEvent } from '@vitest/browser/context'; import { describe, expect, vi } from 'vitest'; import { render } from 'vitest-browser-react'; import { VariantExplorerFilter } from './VariantExplorerFilter'; import { DUMMY_LAPIS_URL, type LapisRouteMocker } from '../../../../../routeMocker'; import { it } from '../../../../../test-extend'; +import type { CollectionSummary } from '../../../../types/Collection'; import type { WasapVariantFilter } from '../../../views/wasap/wasapPageConfig'; const DUMMY_LAPIS_URL_2 = 'http://lapis2.dummy'; +const DUMMY_COLLECTIONS: CollectionSummary[] = [ + { id: 1, name: 'XBB.1.5', ownedBy: 1, organism: 'SARS-CoV-2', description: null, variantCount: 5 }, + { id: 2, name: 'JN.1', ownedBy: 1, organism: 'SARS-CoV-2', description: null, variantCount: 3 }, +]; +const mockPredefinedQueryResult = { data: DUMMY_COLLECTIONS } as unknown as UseQueryResult; + describe('VariantExplorerFilter', () => { const defaultPageState: WasapVariantFilter = { mode: 'variant', + signatureType: 'computed', sequenceType: 'nucleotide', variant: undefined, minProportion: 0.05, @@ -20,6 +29,11 @@ describe('VariantExplorerFilter', () => { timeFrame: 'all', }; + const predefinedPageState: WasapVariantFilter = { + ...defaultPageState, + signatureType: 'predefined', + }; + it('calls setPageState when changing sequence type', async ({ routeMockers: { lapis } }) => { setupLapisMocks(lapis); const mockSetPageState = vi.fn(); @@ -98,6 +112,87 @@ describe('VariantExplorerFilter', () => { minProportion: 0.1, }); }); + + it('calls setPageState when switching to predefined signature type', async ({ routeMockers: { lapis } }) => { + setupLapisMocks(lapis); + const mockSetPageState = vi.fn(); + + render( + + + , + ); + + const variantSourceSelect = page.getByRole('combobox').first(); + await variantSourceSelect.selectOptions('predefined'); + + expect(mockSetPageState).toHaveBeenCalledWith({ + ...defaultPageState, + signatureType: 'predefined', + }); + }); + + it('calls setPageState when selecting a predefined collection', async ({ routeMockers: { lapis } }) => { + setupLapisMocks(lapis); + const mockSetPageState = vi.fn(); + + const { getByRole } = render( + + + , + ); + + const collectionInput = page.getByPlaceholder('Select variant'); + await collectionInput.click(); + await userEvent.type(collectionInput, 'XBB'); + + const option = await vi.waitFor(() => getByRole('option', { name: 'XBB.1.5', exact: true })); + await option.click(); + + await vi.waitFor(() => { + expect(mockSetPageState).toHaveBeenCalledWith({ + ...predefinedPageState, + collectionId: 1, + }); + }); + }); + + it('calls setPageState when toggling "Mutation not in parent"', async ({ routeMockers: { lapis } }) => { + setupLapisMocks(lapis); + const mockSetPageState = vi.fn(); + + const { getByLabelText } = render( + + + , + ); + + const checkbox = getByLabelText('Mutation not in parent'); + await checkbox.click(); + + expect(mockSetPageState).toHaveBeenCalledWith({ + ...predefinedPageState, + newMutationsOnly: true, + }); + }); }); function setupLapisMocks(lapisRouteMocker: LapisRouteMocker) { diff --git a/website/src/components/pageStateSelectors/wasap/filters/VariantExplorerFilter.tsx b/website/src/components/pageStateSelectors/wasap/filters/VariantExplorerFilter.tsx index 635f01fb7..6739cf1b5 100644 --- a/website/src/components/pageStateSelectors/wasap/filters/VariantExplorerFilter.tsx +++ b/website/src/components/pageStateSelectors/wasap/filters/VariantExplorerFilter.tsx @@ -1,13 +1,19 @@ +import { type UseQueryResult } from '@tanstack/react-query'; +import { useId } from 'react'; + import { Inset } from '../../../../styles/Inset'; +import { type CollectionSummary } from '../../../../types/Collection'; import { GsLineageFilter } from '../../../genspectrum/GsLineageFilter'; import { VARIANT_TIME_FRAME, variantTimeFrameLabel, + type SignatureType, type VariantTimeFrame, type WasapVariantFilter, } from '../../../views/wasap/wasapPageConfig'; import { SelectorHeadline } from '../../SelectorHeadline'; import { DefineClinicalSignatureInfo } from '../InfoBlocks'; +import { CollectionCombobox } from '../utils/CollectionCombobox'; import { LabeledField } from '../utils/LabeledField'; import { NumericInput } from '../utils/NumericInput'; import { SequenceTypeSelector } from '../utils/SequenceTypeSelector'; @@ -21,6 +27,8 @@ interface VariantExplorerFilterProps { */ clinicalSequenceLapisBaseUrl: string; clinicalSequenceLapisLineageField: string; + predefinedVariantsQueryResult?: UseQueryResult; + predefinedVariantsLabel?: string; } export function VariantExplorerFilter({ @@ -28,69 +36,148 @@ export function VariantExplorerFilter({ setPageState, clinicalSequenceLapisBaseUrl, clinicalSequenceLapisLineageField, + predefinedVariantsQueryResult, + predefinedVariantsLabel = 'Predefined', }: VariantExplorerFilterProps) { + const handleSignatureTypeChange = (newType: SignatureType) => { + setPageState({ ...pageState, signatureType: newType }); + }; + return ( <> setPageState({ ...pageState, sequenceType })} /> - - }>Define Clinical Signature - - - { - setPageState({ ...pageState, variant: lineages[clinicalSequenceLapisLineageField] }); - }} - hideCounts={true} - /> - - - setPageState({ ...pageState, minProportion: v })} - /> - setPageState({ ...pageState, minCount: Math.round(v) })} - /> - setPageState({ ...pageState, minJaccard: v })} - /> - + {predefinedVariantsQueryResult !== undefined && ( + - + )} + {pageState.signatureType === 'predefined' && ( + + )} + {pageState.signatureType === 'computed' && ( + + }> + Define Clinical Signature + + + + { + setPageState({ + ...pageState, + variant: lineages[clinicalSequenceLapisLineageField], + }); + }} + hideCounts={true} + /> + + + setPageState({ ...pageState, minProportion: v })} + /> + setPageState({ ...pageState, minCount: Math.round(v) })} + /> + setPageState({ ...pageState, minJaccard: v })} + /> + + + + + )} ); } + +function PredefinedSignature({ + pageState, + setPageState, + predefinedVariantsQueryResult, +}: { + pageState: WasapVariantFilter; + setPageState: (newState: WasapVariantFilter) => void; + predefinedVariantsQueryResult: UseQueryResult | undefined; +}) { + const collections = predefinedVariantsQueryResult?.data ?? []; + const selectedCollection = collections.find((c) => c.id === pageState.collectionId) ?? null; + const newMutationsCheckBoxId = useId(); + + return ( + + + setPageState({ ...pageState, collectionId: c?.id })} + /> + +
    + setPageState({ ...pageState, newMutationsOnly: e.target.checked })} + /> +
    + +
    +
    +     + ); +} diff --git a/website/src/components/pageStateSelectors/wasap/utils/CollectionCombobox.browser.spec.tsx b/website/src/components/pageStateSelectors/wasap/utils/CollectionCombobox.browser.spec.tsx new file mode 100644 index 000000000..1e887fbd9 --- /dev/null +++ b/website/src/components/pageStateSelectors/wasap/utils/CollectionCombobox.browser.spec.tsx @@ -0,0 +1,155 @@ +import { userEvent } from '@vitest/browser/context'; +import { describe, expect, vi } from 'vitest'; +import { render } from 'vitest-browser-react'; + +import { CollectionCombobox } from './CollectionCombobox'; +import { it } from '../../../../../test-extend'; +import type { CollectionSummary } from '../../../../types/Collection'; + +const makeCollection = (id: number, name: string): CollectionSummary => ({ + id, + name, + ownedBy: 1, + organism: 'test', + description: null, + variantCount: 0, +}); + +const collections = [makeCollection(1, 'Alpha'), makeCollection(2, 'Beta'), makeCollection(3, 'Gamma')]; + +describe('CollectionCombobox', () => { + describe('onInputBlur', () => { + it('calls onChange(null) when blurred with empty input', async () => { + const onChange = vi.fn(); + const { getByRole } = render( + , + ); + + await getByRole('combobox').fill(''); + await userEvent.tab(); + + expect(onChange).toHaveBeenCalledWith(null); + }); + + it('calls onChange with matched collection when blurred with an exact name', async () => { + const onChange = vi.fn(); + const { getByRole } = render( + , + ); + + await getByRole('combobox').fill('Beta'); + await userEvent.tab(); + + expect(onChange).toHaveBeenCalledWith(collections[1]); + }); + + it('calls onChange with matched collection when input has surrounding whitespace', async () => { + const onChange = vi.fn(); + const { getByRole } = render( + , + ); + + await getByRole('combobox').fill(' Beta '); + await userEvent.tab(); + + expect(onChange).toHaveBeenCalledWith(collections[1]); + }); + + it('shows error state and does not call onChange when blurred with an unrecognised name', async () => { + const onChange = vi.fn(); + const { getByRole } = render( + , + ); + + await getByRole('combobox').fill('Unknown'); + await userEvent.tab(); + + expect(onChange).not.toHaveBeenCalled(); + const wrapper = getByRole('combobox').element().closest('.input'); + await expect.element(wrapper as HTMLElement).toHaveClass('input-error'); + }); + + it('clears error state when user starts typing after an invalid blur', async () => { + const onChange = vi.fn(); + const { getByRole } = render( + , + ); + + await getByRole('combobox').fill('Unknown'); + await userEvent.tab(); + + const wrapper = getByRole('combobox').element().closest('.input'); + await expect.element(wrapper as HTMLElement).toHaveClass('input-error'); + + await getByRole('combobox').fill('A'); + await expect.element(wrapper as HTMLElement).not.toHaveClass('input-error'); + }); + }); + + describe('clear button', () => { + it('is not rendered when input is empty', () => { + const { getByLabelText } = render( + , + ); + + expect(getByLabelText('clear selection').elements()).toHaveLength(0); + }); + + it('is visible when a value is selected', async () => { + const { getByLabelText } = render( + , + ); + + await expect.element(getByLabelText('clear selection')).toBeVisible(); + }); + + it('clears the input and calls onChange(null) when clicked', async () => { + const onChange = vi.fn(); + const { getByLabelText, getByRole } = render( + , + ); + + await getByLabelText('clear selection').click(); + + expect(onChange).toHaveBeenCalledWith(null); + await expect.element(getByRole('combobox')).toHaveValue(''); + }); + + it('disappears after being clicked', async () => { + const onChange = vi.fn(); + const { getByLabelText } = render( + , + ); + + await getByLabelText('clear selection').click(); + + expect(getByLabelText('clear selection').elements()).toHaveLength(0); + }); + }); + + describe('filtering', () => { + it('shows only matching items when typing', async () => { + const { getByRole, getByText } = render( + , + ); + + await getByRole('button', { name: 'toggle menu' }).click(); + await getByRole('combobox').fill('Al'); + + await expect.element(getByText('Alpha')).toBeVisible(); + expect(getByText('Beta').elements()).toHaveLength(0); + expect(getByText('Gamma').elements()).toHaveLength(0); + }); + + it('shows "No variants found" when no collections match the input', async () => { + const { getByRole, getByText } = render( + , + ); + + await getByRole('button', { name: 'toggle menu' }).click(); + await getByRole('combobox').fill('zzz'); + + await expect.element(getByText('No variants found.')).toBeVisible(); + }); + }); +}); diff --git a/website/src/components/pageStateSelectors/wasap/utils/CollectionCombobox.tsx b/website/src/components/pageStateSelectors/wasap/utils/CollectionCombobox.tsx new file mode 100644 index 000000000..cb22c2ada --- /dev/null +++ b/website/src/components/pageStateSelectors/wasap/utils/CollectionCombobox.tsx @@ -0,0 +1,127 @@ +import { useCombobox } from 'downshift'; +import { useMemo, useRef, useState } from 'react'; + +import { type CollectionSummary } from '../../../../types/Collection'; + +export function CollectionCombobox({ + collections, + value, + onChange, + placeholderText = 'Select variant', +}: { + collections: CollectionSummary[]; + value: CollectionSummary | null; + onChange: (item: CollectionSummary | null) => void; + placeholderText?: string; +}) { + const [inputFilter, setInputFilter] = useState(() => value?.name ?? ''); + const [inputIsInvalid, setInputIsInvalid] = useState(false); + + const sortedCollections = useMemo( + () => [...collections].sort((a, b) => a.name.localeCompare(b.name)), + [collections], + ); + + const filteredCollections = useMemo( + () => sortedCollections.filter((c) => c.name.toLowerCase().includes(inputFilter.toLowerCase())), + [sortedCollections, inputFilter], + ); + + const buttonRef = useRef(null); + + const { + isOpen, + getToggleButtonProps, + getMenuProps, + getInputProps, + highlightedIndex, + getItemProps, + inputValue, + closeMenu, + reset, + } = useCombobox({ + items: filteredCollections, + itemToString: (item) => item?.name ?? '', + selectedItem: value, + onInputValueChange({ inputValue }) { + setInputIsInvalid(false); + setInputFilter(inputValue.trim()); + }, + onSelectedItemChange({ selectedItem }) { + onChange(selectedItem ?? null); + }, + }); + + const onInputBlur = () => { + if (inputValue === '') { + onChange(null); + return; + } + const match = collections.find((c) => c.name === inputValue.trim()); + if (match !== undefined) { + onChange(match); + return; + } + setInputIsInvalid(true); + }; + + return ( +
    +
    { + if (e.relatedTarget !== buttonRef.current) { + closeMenu(); + } + }} + > + + {inputValue !== '' && ( + + )} + +
    +
      + {filteredCollections.length > 0 ? ( + filteredCollections.map((item, index) => ( +
    • + {item.name} +
      • + )) + ) : ( +
    • No variants found.
      • + )} +
    +
    + ); +} diff --git a/website/src/components/views/wasap/WasapPage.tsx b/website/src/components/views/wasap/WasapPage.tsx index 85b5be6a4..f7de97c3e 100644 --- a/website/src/components/views/wasap/WasapPage.tsx +++ b/website/src/components/views/wasap/WasapPage.tsx @@ -1,15 +1,8 @@ -import { useMemo } from 'react'; +import { useEffect, useMemo } from 'react'; import { type FC } from 'react'; -import { CollectionInfo } from './components/CollectionInfo'; -import { NoDataHelperText } from './components/NoDataHelperText'; -import { VariantFetchInfo } from './components/VariantFetchInfo'; -import { WasapStats } from './components/WasapStats'; -import { getInitialMeanProportionInterval } from './initialMeanProportionInterval'; -import type { ResistanceData } from './resistanceData'; -import { useWasapPageData } from './useWasapPageData'; -import type { WasapPageConfig } from './wasapPageConfig'; import { withQueryProvider } from '../../../backendApi/withQueryProvider'; +import { getClientLogger } from '../../../clientLogger'; import { defaultBreadcrumbs } from '../../../layouts/Breadcrumbs.tsx'; import { DataPageLayout } from '../../../layouts/OrganismPage/DataPageLayout.tsx'; import { dataOrigins } from '../../../types/dataOrigins.ts'; @@ -20,6 +13,16 @@ import { GsMutationsOverTime } from '../../genspectrum/GsMutationsOverTime'; import { GsQueriesOverTime } from '../../genspectrum/GsQueriesOverTime.tsx'; import { WasapPageStateSelector } from '../../pageStateSelectors/wasap/WasapPageStateSelector'; import { usePageState } from '../usePageState.ts'; +import { CollectionInfo } from './components/CollectionInfo'; +import { NoDataHelperText } from './components/NoDataHelperText'; +import { VariantFetchInfo } from './components/VariantFetchInfo'; +import { WasapStats } from './components/WasapStats'; +import { getInitialMeanProportionInterval } from './initialMeanProportionInterval'; +import type { ResistanceData } from './resistanceData'; +import { useWasapPageData } from './useWasapPageData'; +import type { WasapPageConfig } from './wasapPageConfig'; + +const logger = getClientLogger('WasapPage'); export type WasapPageProps = { config: WasapPageConfig; @@ -37,7 +40,13 @@ export const WasapPageInner: FC = ({ config, resistanceData }) = const { mutationAnnotations, displayMutationsBySet } = resistanceData; // fetch which mutations should be analyzed - const { data, isPending, isError } = useWasapPageData(config, displayMutationsBySet, analysis); + const { data, isPending, isError, error } = useWasapPageData(config, displayMutationsBySet, analysis); + + useEffect(() => { + if (error) { + logger.error(`Failed to fetch wasap page data: ${error instanceof Error ? error.message : String(error)}`); + } + }, [error]); const initialMeanProportionInterval = getInitialMeanProportionInterval(analysis); @@ -77,7 +86,16 @@ export const WasapPageInner: FC = ({ config, resistanceData }) = />
    {isError ? ( - There was an error fetching the data to display. + analysis.mode === 'variant' && + analysis.signatureType === 'predefined' && + analysis.collectionId === undefined ? ( +
    +

    No variant selected

    +

    Please select a variant from the filter panel.

    +
    + ) : ( + There was an error fetching the data to display. + ) ) : isPending ? ( ) : ( @@ -101,15 +119,17 @@ export const WasapPageInner: FC = ({ config, resistanceData }) = customColumns={data.customColumns} /> )} - {analysis.mode === 'variant' && config.variantAnalysisModeEnabled && ( - - )} + {analysis.mode === 'variant' && + analysis.signatureType === 'computed' && + config.variantAnalysisModeEnabled && ( + + )} ) : ( <> diff --git a/website/src/components/views/wasap/initialMeanProportionInterval.spec.ts b/website/src/components/views/wasap/initialMeanProportionInterval.spec.ts index 03f38a240..521a2e8d9 100644 --- a/website/src/components/views/wasap/initialMeanProportionInterval.spec.ts +++ b/website/src/components/views/wasap/initialMeanProportionInterval.spec.ts @@ -27,6 +27,7 @@ describe('getInitialMeanProportionInterval', () => { test('other analysis states initially show the full mean proportion range', () => { const analysis: WasapAnalysisFilter = { mode: 'variant', + signatureType: 'computed', sequenceType: 'nucleotide', variant: 'XFG*', minProportion: 0.8, diff --git a/website/src/components/views/wasap/useWasapPageData.ts b/website/src/components/views/wasap/useWasapPageData.ts index 5799daf5e..9d69bde1e 100644 --- a/website/src/components/views/wasap/useWasapPageData.ts +++ b/website/src/components/views/wasap/useWasapPageData.ts @@ -12,6 +12,7 @@ import type { WasapUntrackedFilter, WasapVariantFilter, } from './wasapPageConfig'; +import { getBackendServiceForClientside } from '../../../backendApi/backendService'; import { getCollection } from '../../../covspectrum/getCollection'; import { detailedMutationsToQuery } from '../../../covspectrum/variantConversionUtil'; import { getCladeLineages } from '../../../lapis/getCladeLineages'; @@ -68,6 +69,21 @@ function fetchManualModeData(config: WasapPageConfig, analysis: WasapManualFilte async function fetchVariantModeData( config: WasapPageConfig, analysis: WasapVariantFilter, +): Promise { + if (!config.variantAnalysisModeEnabled) { + throw Error("Cannot fetch data, 'variant' mode is not enabled."); + } + switch (analysis.signatureType) { + case 'computed': + return fetchVariantComputedModeData(config, analysis); + case 'predefined': + return fetchVariantPredefinedModeData(analysis); + } +} + +async function fetchVariantComputedModeData( + config: WasapPageConfig, + analysis: WasapVariantFilter, ): Promise { if (!config.variantAnalysisModeEnabled) { throw Error("Cannot fetch data, 'variant' mode is not enabled."); @@ -97,6 +113,36 @@ async function fetchVariantModeData( }; } +async function fetchVariantPredefinedModeData(analysis: WasapVariantFilter): Promise { + if (analysis.collectionId === undefined) { + throw new Error('No collection selected for predefined variant mode.'); + } + const collection = await getBackendServiceForClientside().getCollection({ id: String(analysis.collectionId) }); + + // These names match the variant names hardcoded in the collection seeder. + let variantName: string; + if (analysis.sequenceType === 'nucleotide') { + variantName = analysis.newMutationsOnly ? 'New nucleotide substitutions' : 'Nucleotide substitutions'; + } else { + variantName = analysis.newMutationsOnly ? 'New amino acid substitutions' : 'Amino acid substitutions'; + } + + const variant = collection.variants.find((v) => v.name === variantName); + if (!variant) { + throw new Error(`Variant "${variantName}" not found in collection ${collection.id}.`); + } + if (variant.type !== 'filterObject') { + throw new Error(`Variant "${variantName}" in collection ${collection.id} is not a filterObject variant.`); + } + + const mutations = + analysis.sequenceType === 'nucleotide' + ? (variant.filterObject.nucleotideMutations ?? []) + : (variant.filterObject.aminoAcidMutations ?? []); + + return { type: 'mutations', displayMutations: mutations }; +} + function fetchResistanceModeData( displayMutationsBySet: Record, analysis: WasapResistanceFilter, diff --git a/website/src/components/views/wasap/wasapPageConfig.ts b/website/src/components/views/wasap/wasapPageConfig.ts index 2c4cbfe69..3cde304db 100644 --- a/website/src/components/views/wasap/wasapPageConfig.ts +++ b/website/src/components/views/wasap/wasapPageConfig.ts @@ -9,6 +9,11 @@ export type WasapPageConfig = WasapPageConfigBase & AnalysisModeConfigs; * Base settings that apply to all modes. */ export type WasapPageConfigBase = { + /** + * The internal identifier of the organism, i.e. 'covid'. Used as a key in maps and API parameters. + */ + internalName: string; + /** * The name of the organism, i.e. 'Sars-CoV-2' */ @@ -70,6 +75,11 @@ type VariantAnalysisModeConfig = } | { variantAnalysisModeEnabled: true; + predefinedVariantsSource?: { + collectionsUserId: number; + collectionsTag: string; + variantSourceLabel?: string; + }; clinicalLapis: { lapisBaseUrl: string; dateField: string; @@ -195,14 +205,25 @@ export function variantTimeFrameLabel(timeFrame: VariantTimeFrame): string { } } +/** + * The type of variant mutation signature. `predefined` is a pre-defined list pulled from online, + * `computed` computes the list of signature mutations for a variant based on user parameters. + */ +export type SignatureType = 'computed' | 'predefined'; + export type WasapVariantFilter = { mode: 'variant'; + signatureType: SignatureType; sequenceType: SequenceType; + // computed signature fields variant?: string; minProportion: number; minCount: number; minJaccard: number; timeFrame: VariantTimeFrame; + // predefined signature fields + collectionId?: number; + newMutationsOnly?: boolean; }; export type WasapResistanceFilter = { diff --git a/website/src/types/wastewaterConfig.ts b/website/src/types/wastewaterConfig.ts index 8e10fa1d5..949d28601 100644 --- a/website/src/types/wastewaterConfig.ts +++ b/website/src/types/wastewaterConfig.ts @@ -15,6 +15,7 @@ export const wastewaterPathFragment = 'swiss-wastewater'; export const wastewaterOrganismConfigs: Record = { [wastewaterOrganisms.covid]: { + internalName: wastewaterOrganisms.covid, name: 'SARS-CoV-2', path: `/${wastewaterPathFragment}/covid`, description: 'Analyze SARS-CoV-2 data that was collected by the WISE project.', @@ -56,6 +57,11 @@ export const wastewaterOrganismConfigs: Record { 'granularity=week&' + 'analysisMode=variant&' + 'sequenceType=nucleotide&' + + 'signatureType=computed&' + 'variant=BA.2*&' + 'minProportion=0.5&' + 'minCount=10&' + @@ -267,6 +270,56 @@ describe('WasapPageStateHandler', () => { expect(analysis2.minProportion).toBe(analysis1.minProportion); expect(analysis2.minJaccard).toBe(analysis1.minJaccard); }); + + it('defaults signatureType to computed when absent from URL', () => { + const url = '/wastewater/covid?analysisMode=variant&'; + const filter = handler.parsePageStateFromUrl(new URL(`http://example.com${url}`)); + + const analysis = filter.analysis as WasapVariantFilter; + expect(analysis.signatureType).toBe('computed'); + }); + + it('parses and encodes predefined variant filter with collectionId (round-trip)', () => { + const url = + '/wastewater/covid?' + + 'locationName=Z%C3%BCrich+%28ZH%29&' + + 'granularity=day&' + + 'analysisMode=variant&' + + 'sequenceType=nucleotide&' + + 'signatureType=predefined&' + + 'collectionId=42&'; + const filter = handler.parsePageStateFromUrl(new URL(`http://example.com${url}`)); + + expect(filter.analysis.mode).toBe('variant'); + const analysis = filter.analysis as WasapVariantFilter; + expect(analysis.signatureType).toBe('predefined'); + expect(analysis.collectionId).toBe(42); + expect(analysis.newMutationsOnly).toBe(false); + + const newUrl = handler.toUrl(filter); + expect(newUrl).toBe(url); + }); + + it('parses and encodes newMutationsOnly=true in predefined variant mode (round-trip)', () => { + const url = + '/wastewater/covid?' + + 'locationName=Z%C3%BCrich+%28ZH%29&' + + 'granularity=day&' + + 'analysisMode=variant&' + + 'sequenceType=nucleotide&' + + 'signatureType=predefined&' + + 'collectionId=42&' + + 'newMutationsOnly=true&'; + const filter = handler.parsePageStateFromUrl(new URL(`http://example.com${url}`)); + + expect(filter.analysis.mode).toBe('variant'); + const analysis = filter.analysis as WasapVariantFilter; + expect(analysis.signatureType).toBe('predefined'); + expect(analysis.newMutationsOnly).toBe(true); + + const newUrl = handler.toUrl(filter); + expect(newUrl).toBe(url); + }); }); describe('resistance mode', () => { diff --git a/website/src/views/pageStateHandlers/WasapPageStateHandler.ts b/website/src/views/pageStateHandlers/WasapPageStateHandler.ts index 37f6909a4..f4b4569ad 100644 --- a/website/src/views/pageStateHandlers/WasapPageStateHandler.ts +++ b/website/src/views/pageStateHandlers/WasapPageStateHandler.ts @@ -7,6 +7,7 @@ import type { BaselineFilterConfig } from '../../components/pageStateSelectors/B import { enabledAnalysisModes, type ExcludeSetName, + type SignatureType, type VariantTimeFrame, type WasapAnalysisFilter, type WasapAnalysisMode, @@ -52,12 +53,15 @@ export class WasapPageStateHandler implements PageStateHandler { mutations: texts.mutations?.split('|'), }; break; - case 'variant': + case 'variant': { if (!this.config.variantAnalysisModeEnabled) { throw Error("The 'variant' analysis mode is not enabled."); } analysis = { mode, + signatureType: + (texts.signatureType as SignatureType | undefined) ?? + this.config.filterDefaults.variant.signatureType, sequenceType: providedSequenceType ?? this.config.filterDefaults.variant.sequenceType, variant: texts.variant ?? this.config.filterDefaults.variant.variant, minProportion: Number(texts.minProportion ?? this.config.filterDefaults.variant.minProportion), @@ -66,8 +70,13 @@ export class WasapPageStateHandler implements PageStateHandler { timeFrame: (texts.timeFrame as VariantTimeFrame | undefined) ?? this.config.filterDefaults.variant.timeFrame, + collectionId: texts.collectionId + ? Number(texts.collectionId) + : this.config.filterDefaults.variant.collectionId, + newMutationsOnly: texts.newMutationsOnly === 'true', }; break; + } case 'resistance': if (!this.config.resistanceAnalysisModeEnabled) { throw Error("The 'resistance' analysis mode is not enabled."); @@ -135,11 +144,23 @@ export class WasapPageStateHandler implements PageStateHandler { break; case 'variant': setSearchFromString(search, 'sequenceType', analysis.sequenceType); - setSearchFromString(search, 'variant', analysis.variant); - setSearchFromString(search, 'minProportion', String(analysis.minProportion)); - setSearchFromString(search, 'minCount', String(analysis.minCount)); - setSearchFromString(search, 'minJaccard', String(analysis.minJaccard)); - setSearchFromString(search, 'timeFrame', analysis.timeFrame); + setSearchFromString(search, 'signatureType', analysis.signatureType); + if (analysis.signatureType === 'predefined') { + setSearchFromString( + search, + 'collectionId', + analysis.collectionId ? String(analysis.collectionId) : undefined, + ); + if (analysis.newMutationsOnly) { + setSearchFromString(search, 'newMutationsOnly', 'true'); + } + } else { + setSearchFromString(search, 'variant', analysis.variant); + setSearchFromString(search, 'minProportion', String(analysis.minProportion)); + setSearchFromString(search, 'minCount', String(analysis.minCount)); + setSearchFromString(search, 'minJaccard', String(analysis.minJaccard)); + setSearchFromString(search, 'timeFrame', analysis.timeFrame); + } break; case 'resistance': setSearchFromString(search, 'resistanceSet', analysis.resistanceSet); @@ -236,5 +257,13 @@ function generateWasapFilterConfig(pageConfig: WasapPageConfig): BaselineFilterC type: 'text', lapisField: 'collectionId', }, + { + type: 'text', + lapisField: 'signatureType', + }, + { + type: 'text', + lapisField: 'newMutationsOnly', + }, ]; } diff --git a/website/tests/ViewPage.ts b/website/tests/ViewPage.ts index b2988f69b..27aaaf547 100644 --- a/website/tests/ViewPage.ts +++ b/website/tests/ViewPage.ts @@ -2,6 +2,11 @@ import { expect, type Locator, type Page } from '@playwright/test'; import { type Organism } from '../src/types/Organism.ts'; +export async function expectToSeeNoComponentErrors(page: Page) { + await expect(page.getByText('Error -', { exact: false })).not.toBeVisible(); + await expect(page.getByText('Something went wrong', { exact: false })).not.toBeVisible(); +} + export abstract class ViewPage { constructor(public readonly page: Page) {} @@ -16,8 +21,7 @@ export abstract class ViewPage { } public async expectToSeeNoComponentErrors() { - await expect(this.page.getByText('Error -', { exact: false })).not.toBeVisible(); - await expect(this.page.getByText('Something went wrong', { exact: false })).not.toBeVisible(); + await expectToSeeNoComponentErrors(this.page); } public async selectDateRange(dateRangeOption: string) { diff --git a/website/tests/WasapPage.ts b/website/tests/WasapPage.ts new file mode 100644 index 000000000..6c44db876 --- /dev/null +++ b/website/tests/WasapPage.ts @@ -0,0 +1,44 @@ +import { type Page } from '@playwright/test'; + +import { expectToSeeNoComponentErrors } from './ViewPage.ts'; +import { type WastewaterOrganismName, wastewaterOrganismConfigs } from '../src/types/wastewaterConfig.ts'; + +export class WasapPage { + constructor(public readonly page: Page) {} + + public async goto(organism: WastewaterOrganismName) { + await this.page.goto(wastewaterOrganismConfigs[organism].path); + } + + public async submitFilters() { + await this.page.getByRole('button', { name: 'Apply filters' }).click(); + } + + public get mutationsOverTimeHeading() { + return this.page.getByRole('heading', { name: 'mutations over time' }); + } + + public get filterDatasetHeading() { + return this.page.getByRole('heading', { name: 'Filter dataset' }); + } + + public get mutationSelectionHeading() { + return this.page.getByRole('heading', { name: 'Mutation selection' }); + } + + public get analysisModeSelect() { + return this.page.locator('select').filter({ has: this.page.locator('option', { hasText: 'Manual' }) }); + } + + public async selectAnalysisMode(mode: string) { + await this.analysisModeSelect.selectOption({ label: mode }); + } + + public async selectGranularity(granularity: 'Day' | 'Week') { + await this.page.getByText(granularity, { exact: true }).click(); + } + + public async expectToSeeNoComponentErrors() { + await expectToSeeNoComponentErrors(this.page); + } +} diff --git a/website/tests/e2e.fixture.ts b/website/tests/e2e.fixture.ts index daa12ab8d..cecf7f4b2 100644 --- a/website/tests/e2e.fixture.ts +++ b/website/tests/e2e.fixture.ts @@ -6,6 +6,7 @@ import { CompareVariantsPage } from './CompareVariantsPage.ts'; import { LandingPage } from './LandingPage.ts'; import { SequencingEffortsPage } from './SequencingEffortsPage.ts'; import { SingleVariantPage } from './SingleVariantPage.ts'; +import { WasapPage } from './WasapPage.ts'; import { ApiKeyPage } from './api-key/ApiKeyPage.ts'; import { CollectionDetailPage } from './collections/CollectionDetailPage.ts'; import { CollectionFormPage } from './collections/CollectionFormPage.ts'; @@ -20,6 +21,7 @@ type E2EFixture = { compareSideBySidePage: CompareSideBySidePage; singleVariantPage: SingleVariantPage; landingPage: LandingPage; + wasapPage: WasapPage; collectionDetailPage: CollectionDetailPage; collectionFormPage: CollectionFormPage; authenticatedPage: Page; @@ -46,6 +48,9 @@ export const test = base.extend({ landingPage: async ({ page }, use) => { await use(new LandingPage(page)); }, + wasapPage: async ({ page }, use) => { + await use(new WasapPage(page)); + }, collectionDetailPage: async ({ page }, use) => { await use(new CollectionDetailPage(page)); }, diff --git a/website/tests/wastewater.spec.ts b/website/tests/wastewater.spec.ts new file mode 100644 index 000000000..39d284d46 --- /dev/null +++ b/website/tests/wastewater.spec.ts @@ -0,0 +1,77 @@ +import { expect } from '@playwright/test'; + +import { expectToSeeNoComponentErrors } from './ViewPage.ts'; +import { test } from './e2e.fixture.ts'; +import { wastewaterOrganismConfigs, wastewaterOrganisms } from '../src/types/wastewaterConfig.ts'; + +test.describe('The Swiss Wastewater Overview Page', () => { + test('should show heading and links to all wastewater pages', async ({ page }) => { + await page.goto('/swiss-wastewater'); + + await expect(page).toHaveTitle('Swiss Wastewater'); + await expect(page.getByRole('heading', { name: 'Swiss Wastewater', level: 1 })).toBeVisible(); + + await expect(page.getByRole('link', { name: /^SARS-CoV-2 Analyze/ })).toBeVisible(); + await expect(page.getByRole('link', { name: /^RSV-A Analyze/ })).toBeVisible(); + await expect(page.getByRole('link', { name: /^RSV-B Analyze/ })).toBeVisible(); + await expect(page.getByRole('link', { name: /^RSV \(non-interactive\)/ })).toBeVisible(); + await expect(page.getByRole('link', { name: /^Influenza \(non-interactive\)/ })).toBeVisible(); + }); +}); + +test.describe('WASAP Pages', () => { + test.setTimeout(60_000); + + for (const organism of Object.values(wastewaterOrganisms)) { + const { name } = wastewaterOrganismConfigs[organism]; + + test.describe(name, () => { + test('should load with default filters and show mutation data', async ({ wasapPage }) => { + await wasapPage.goto(organism); + + await expect(wasapPage.page).toHaveTitle(`Swiss wastewater - ${name}`); + await expect(wasapPage.filterDatasetHeading).toBeVisible(); + await expect(wasapPage.mutationSelectionHeading).toBeVisible(); + + await wasapPage.expectToSeeNoComponentErrors(); + + await expect(wasapPage.mutationsOverTimeHeading).toBeVisible(); + }); + + test('should show mutation data after changing and applying filters', async ({ wasapPage }) => { + await wasapPage.goto(organism); + + await wasapPage.selectAnalysisMode('Variant Explorer'); + await wasapPage.selectGranularity('Week'); + await wasapPage.submitFilters(); + + await wasapPage.expectToSeeNoComponentErrors(); + await expect(wasapPage.mutationsOverTimeHeading).toBeVisible(); + }); + }); + } +}); + +test.describe('Non-interactive Wastewater Pages', () => { + test.setTimeout(60_000); + + test('RSV page should render with RSV-A and RSV-B sections', async ({ page }) => { + await page.goto('/swiss-wastewater/rsv', { timeout: 60_000 }); + + await expect(page).toHaveTitle('Swiss wastewater - RSV'); + await expect(page.getByRole('heading', { name: 'RSV-A', level: 2, exact: true })).toBeVisible(); + await expect(page.getByRole('heading', { name: 'RSV-B', level: 2, exact: true })).toBeVisible(); + await expectToSeeNoComponentErrors(page); + }); + + test('Influenza page should render with all subtype sections', async ({ page }) => { + await page.goto('/swiss-wastewater/flu', { timeout: 60_000 }); + + await expect(page).toHaveTitle('Swiss wastewater - Influenza'); + await expect(page.getByRole('heading', { name: 'H1', level: 2, exact: true })).toBeVisible(); + await expect(page.getByRole('heading', { name: 'N1', level: 2, exact: true })).toBeVisible(); + await expect(page.getByRole('heading', { name: 'H3', level: 2, exact: true })).toBeVisible(); + await expect(page.getByRole('heading', { name: 'N2', level: 2, exact: true })).toBeVisible(); + await expectToSeeNoComponentErrors(page); + }); +});