diff --git a/FEATURE_BACKLOG.md b/FEATURE_BACKLOG.md index c92e2d95b365fe681eb5d5bcb5c80705d495739c..bcd6e58871caf739127836129125b3dabf054a80 100644 --- a/FEATURE_BACKLOG.md +++ b/FEATURE_BACKLOG.md @@ -56,7 +56,7 @@ Decisions and dependencies for implementation: - Implemented: eukaryotic tree with bounded subtrees and exact, expandable “Other lineages” aggregates; NCBI taxonomy with source checksums and dates; merged IDs resolved. Unresolved taxonomy is excluded from the eukaryotic view. - Implemented: English names beside every scientific name, from NCBI Taxonomy common names plus a curated gloss table (`refresh_common_names.py`). - Remaining: connect the taxonomy inventory to accession-level annotation results and distinguish partial/complete base coverage. -- Remaining: clade icons. [PhyloPic](https://www.phylopic.org) is the usable source and resolves NCBI taxids directly, walking up the tree when a clade has no silhouette of its own: `GET https://api.phylopic.org/resolve/ncbi.nlm.nih.gov/taxid/{taxid}?embed_primaryImage=true` with `Accept: application/vnd.phylopic.v2+json`, which returns an SVG under `_embedded.primaryImage._links.vectorFile.href`. Two things to settle before using it: licences differ per image (CC0, CC BY 4.0, CC BY-SA 3.0 and at least one CC BY-NC-SA 3.0 among the groups the atlas shows first), so each icon needs its own credit line and the non-commercial ones need replacing or omitting; and the SVGs should be fetched once into the repo rather than hot-linked, to keep the Space free of external requests. +- Implemented: clade silhouettes from PhyloPic, filtered to CC0/Public Domain Mark/CC BY at build time (`refresh_icons.py`), with every CC BY artist credited in the interface. ## F003 — Comparison with RefSeq annotations diff --git a/README.md b/README.md index 5a79ca59b281c14c8667ab453f57133880fe1d53..09d32f95ca1344ae08d6dea950367c3894408810 100644 --- a/README.md +++ b/README.md @@ -27,6 +27,8 @@ Click a group to expand its direct lineages into a new column on the right; ever English names come from `data/common_names.json`, built by `refresh_common_names.py` from NCBI Taxonomy's `genbank common name` and `common name` entries (about 9,200 taxa) plus a curated table of roughly 190 short glosses for the large unranked clades NCBI leaves unnamed. Glosses are plain-language summaries of the living members of a clade, not formal synonyms; the scientific name stays the primary label and a gloss that merely repeats it is dropped at build time. Rebuild it with `python refresh_common_names.py` once `.cache/coverage/taxdump.tar.gz` is present; the build fails if a curated taxid no longer matches its scientific name in the snapshot. +Each group also carries a clade silhouette from [PhyloPic](https://www.phylopic.org), fetched by `refresh_icons.py` into `data/icons/` with the map and credits in `data/icons.json`. The fetcher resolves each taxon's NCBI ID to a PhyloPic node and prefers that node's representative image, falling back to a clade search only when the representative one is not free to use. Both searches exclude NonCommercial and ShareAlike images: NC is unsettled for a Space run by a company, and SA would reach into the repository as soon as an icon were adapted. What ships is CC0, Public Domain Mark and CC BY, stored byte-for-byte as PhyloPic serves it, with every CC BY artist credited in the "Silhouette credits" panel. Icons are fetched for groups with at least 100 assemblies; smaller groups borrow their nearest illustrated ancestor at render time. Gradio serves them as static files through `gr.set_static_paths`, so each is cached once by the browser instead of riding along in every re-render. + The graphic uses server-rendered SVG/HTML with scoped styles in `atlas.css` and delegated click/keyboard handlers in `atlas.js`; no external graphics library or image assets are required. Include these files when deploying. The annotation workspace shares the atlas palette and typography through `style.py` and `app.css`: warm panels, serif section headings, green controls, and matching tables, downloads, and disclosures. CDS plots use a solid green positive strand and a dashed warm-brown negative strand; binary labels use green. The fixed light palette stays consistent with the landing graphic under either OS color preference. Include both style files when deploying; Gradio 6 receives the theme and stylesheet in `launch()`. diff --git a/app.css b/app.css index f1becc9ec82a36bdce4b3265526e2e7c29c18232..29f438509eba123de9bd74726f49e70c70352094 100644 --- a/app.css +++ b/app.css @@ -39,11 +39,11 @@ /* Full-width navigation: one equal segment for each view. */ .gradio-container { width:100%!important; min-width:0!important; box-sizing:border-box; } #atlas-navigation { border:0; background:transparent; min-width:0; max-width:100%; } -#atlas-navigation > .tab-wrapper { width:100%; height:auto!important; min-height:76px; border:0!important; box-shadow:none!important; margin:0 0 20px; padding:0; } -#atlas-navigation > .tab-wrapper > .tab-container { display:grid!important; grid-template-columns:repeat(2,minmax(0,1fr)); gap:6px; width:100%!important; height:auto!important; box-sizing:border-box; border:1px solid #dbe3d3!important; border-radius:18px; padding:6px; margin:0; background:#edf2e7; box-shadow:none!important; } -#atlas-navigation > .tab-wrapper > .tab-container > button { display:flex!important; align-items:center; justify-content:center; width:100%; min-width:0; min-height:62px; height:auto!important; box-sizing:border-box; padding:14px 12px; margin:0!important; border:0!important; border-radius:12px; box-shadow:none!important; background:transparent; color:#52694f; font:600 17px/1.3 Arial,Helvetica,sans-serif; white-space:normal; text-align:center; text-decoration:none!important; } -#atlas-navigation > .tab-wrapper > .tab-container > button:hover { background:#e0e9d9; color:#173c30; } -#atlas-navigation > .tab-wrapper > .tab-container > button[aria-selected="true"] { background:#245d45; color:#fffefa; } +#atlas-navigation > .tab-wrapper { width:100%; height:auto!important; min-height:0; border:0!important; box-shadow:none!important; margin:0 0 18px; padding:0; } +#atlas-navigation > .tab-wrapper > .tab-container { display:flex!important; justify-content:flex-start; gap:26px; width:100%!important; height:auto!important; box-sizing:border-box; border:0!important; border-bottom:1px solid #dbe3d3!important; border-radius:0; padding:0; margin:0; background:transparent; box-shadow:none!important; } +#atlas-navigation > .tab-wrapper > .tab-container > button { display:inline-flex!important; align-items:center; justify-content:flex-start; width:auto; min-width:0; min-height:0; height:auto!important; box-sizing:border-box; padding:0 2px 11px; margin:0!important; border:0!important; border-bottom:2px solid transparent!important; border-radius:0; box-shadow:none!important; background:transparent; color:#6c7d6a; font:600 14px/1.4 Arial,Helvetica,sans-serif; white-space:nowrap; text-align:left; text-decoration:none!important; transition:color .15s; } +#atlas-navigation > .tab-wrapper > .tab-container > button:hover { background:transparent; color:#173c30; } +#atlas-navigation > .tab-wrapper > .tab-container > button[aria-selected="true"] { background:transparent; color:#173c30; border-bottom-color:#245d45!important; } #atlas-navigation > .tab-wrapper::before, #atlas-navigation > .tab-wrapper::after, #atlas-navigation > .tab-wrapper > .tab-container::before, #atlas-navigation > .tab-wrapper > .tab-container::after, #atlas-navigation > .tab-wrapper > .tab-container > button::before, #atlas-navigation > .tab-wrapper > .tab-container > button::after { content:none!important; display:none!important; } @@ -54,6 +54,6 @@ .database-heading h1 { color:#173c30; font:400 clamp(32px,5vw,48px)/1.1 Georgia,'Times New Roman',serif; letter-spacing:-1px; margin:0 0 12px; } .database-heading p { color:#647467; font:14px/1.6 Arial,Helvetica,sans-serif; margin:0; } @media(max-width:700px) { - #atlas-navigation > .tab-wrapper > .tab-container { gap:4px; padding:4px; border-radius:14px; } - #atlas-navigation > .tab-wrapper > .tab-container > button { font-size:12px; min-height:68px; padding:10px 3px; border-radius:10px; overflow-wrap:anywhere; } + #atlas-navigation > .tab-wrapper > .tab-container { gap:18px; } + #atlas-navigation > .tab-wrapper > .tab-container > button { font-size:13px; padding:0 1px 9px; } } diff --git a/atlas.css b/atlas.css index 42a8b576824869b95eefb707bc59237501cfc485..e3db05658e5eb6d342bcf15b8cda4a75fbb02daa 100644 --- a/atlas.css +++ b/atlas.css @@ -37,12 +37,15 @@ .tree-node.is-selected .bar-outline { stroke:#173c30; stroke-width:1.5; } .tree-node.is-sibling { opacity:.62; transition:opacity .15s; } .tree-node.is-sibling:hover,.tree-node.is-sibling:focus { opacity:1; } +.tree-icon { opacity:.62; transition:opacity .15s; } +.tree-node.is-selected .tree-icon { opacity:.85; } +.tree-node:not(.is-direct):hover .tree-icon { opacity:.9; } .tree-label,.tree-english,.tree-count { paint-order:stroke; stroke:#f7f8f0; stroke-width:4px; stroke-linejoin:round; } .tree-label { font:600 13px Arial,Helvetica,sans-serif; fill:#254735; transition:fill .15s; } .tree-node.is-selected .tree-label { font-weight:700; fill:#173c30; } .tree-english { font:italic 11.5px Georgia,'Times New Roman',serif; fill:#5d7a66; } .tree-count { font:11px Arial,Helvetica,sans-serif; fill:#697966; } -.tree-node:not(.is-direct):hover .tree-label,.tree-node:focus .tree-label { fill:#0f2e22; text-decoration:underline; } +.tree-node:not(.is-direct):hover .tree-label,.tree-node:focus .tree-label { fill:#0f2e22; } .tree-node:not(.is-direct):hover .bar-outline { stroke:#287557; stroke-width:2; } .atlas-footer { display:flex; align-items:center; flex-wrap:wrap; gap:15px; justify-content:space-between; border-top:1px solid #dde4d5; padding-top:14px; color:#6c7a66; font-size:11px; line-height:1.6; } .atlas-legend { display:flex; gap:7px; align-items:center; } diff --git a/data/icons.json b/data/icons.json new file mode 100644 index 0000000000000000000000000000000000000000..f10a3e27231f4de2dad80dd46197ec07a3d880b2 --- /dev/null +++ b/data/icons.json @@ -0,0 +1,4303 @@ +{ + "source": "https://www.phylopic.org", + "build": 558, + "api": "https://api.phylopic.org/resolve/ncbi.nlm.nih.gov/taxid/{taxid} then /images?filter_clade=\u2026&filter_license_nc=false&filter_license_sa=false", + "note": "Silhouettes are stored exactly as PhyloPic serves them, unmodified.", + "minimum_assemblies": 100, + "counts": { + "primary_image": 557, + "assigned": 701, + "clade_fallback": 117, + "unresolved": 392, + "no_free_image": 4, + "distinct_icons": 447, + "bytes": 5891595 + }, + "licenses": { + "https://creativecommons.org/licenses/by/4.0/": 59, + "https://creativecommons.org/publicdomain/zero/1.0/": 297, + "https://creativecommons.org/licenses/by/3.0/": 45, + "https://creativecommons.org/publicdomain/mark/1.0/": 46 + }, + "images": { + "00508809-a509-4330-9e3d-9d3b54248667": { + "license": "https://creativecommons.org/licenses/by/4.0/", + "attribution": "Graham Montgomery", + "contributor": "Graham Montgomery", + "page": "https://www.phylopic.org/images/00508809-a509-4330-9e3d-9d3b54248667", + "ratio": 0.993, + "bytes": 3857 + }, + "0192754b-c8ab-43c0-a475-1a2ad0cfd202": { + "license": "https://creativecommons.org/publicdomain/zero/1.0/", + "attribution": "Anilocra (vectorization by Yan Wong)", + "contributor": "Yan Wong", + "page": "https://www.phylopic.org/images/0192754b-c8ab-43c0-a475-1a2ad0cfd202", + "ratio": 0.544, + "bytes": 2484 + }, + "01a21193-6599-463c-a5f0-75b6fe03189d": { + "license": "https://creativecommons.org/licenses/by/3.0/", + "attribution": "Auckland Museum and T. 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1.16, written by Peter Selinger 2001-2019 + + + + + diff --git a/refresh_icons.py b/refresh_icons.py new file mode 100644 index 0000000000000000000000000000000000000000..5139ca5110d415671e4622cc553c3c4ad78c8aaf --- /dev/null +++ b/refresh_icons.py @@ -0,0 +1,226 @@ +"""Fetch clade silhouettes from PhyloPic for the groups the Genome Atlas shows. + +PhyloPic resolves NCBI taxids directly and walks up its own tree when a clade has +no silhouette of its own, so a request for Eumetazoa answers with the nearest +illustrated ancestor. Two filters are always applied: + +* ``filter_license_nc=false`` drops NonCommercial images. Whether a Space that + sells nothing counts as noncommercial use is genuinely unsettled, and the + question is avoidable: every group in the atlas has a freer alternative. +* ``filter_license_sa=false`` drops ShareAlike images, whose terms would reach + into the repository as soon as an icon were adapted. + +What remains is CC0 and CC BY 4.0. Files are stored exactly as PhyloPic serves +them, unmodified, and ``data/icons.json`` carries the licence and attribution +for each one so the interface can credit the artists. +""" +import argparse +from collections import Counter +import json +import math +from pathlib import Path +import sqlite3 +import time +import urllib.error +import urllib.request + +ROOT = Path(__file__).resolve().parent +API = "https://api.phylopic.org" +HEADERS = {"Accept": "application/vnd.phylopic.v2+json", + "User-Agent": "huggingface-genome-atlas (https://huggingface.co/spaces/HuggingFaceBio/genbank-annotation-explorer)"} +EUKARYOTA = 2759 +COLUMN_LIMIT = 6 +# Groups below this many assemblies inherit an ancestor's icon at render time. +MIN_ASSEMBLIES = 100 +# Columns within this many steps of the root get an icon regardless of size. +SHALLOW_DEPTH = 5 +# The node's representative image almost always wins. Contact sheets of the +# alternatives showed why: for Porifera the representative image is a vase +# sponge, while every other free candidate in the clade is an obscure relative. +# Shape only overrules it past exp(1.4), roughly 4:1, where a silhouette is a +# sliver whatever the renderer does. +PRIMARY_BONUS = 1.4 + + +def get(url, headers=HEADERS, retries=3): + for attempt in range(retries): + try: + with urllib.request.urlopen(urllib.request.Request(url, headers=headers), timeout=60) as response: + return response.read() + except (urllib.error.HTTPError, urllib.error.URLError, TimeoutError) as exc: + if isinstance(exc, urllib.error.HTTPError) and exc.code == 404: + return None + if attempt == retries - 1: + raise + time.sleep(2 * (attempt + 1)) + + +def candidate(image): + """uuid, licence and aspect ratio of an embedded image object.""" + links = image.get("_links") or {} + sizes = (links.get("rasterFiles") or [{}])[0].get("sizes", "") + uuid = image.get("uuid") or links.get("self", {}).get("href", "").removeprefix("/images/").partition("?")[0] + try: + width, height = (int(part) for part in sizes.split("x")) + except ValueError: + return None + if not uuid or not height: + return None + return {"uuid": uuid, "license": links.get("license", {}).get("href", ""), "ratio": width / height} + + +def shape_score(found): + """Distance from square, symmetric in either direction.""" + return abs(math.log(found["ratio"])) + + +def is_free(license_url): + """CC0, Public Domain Mark and plain CC BY only; no NonCommercial, no ShareAlike.""" + return bool(license_url) and "-nc" not in license_url and "-sa" not in license_url + + +def get_json(url): + body = get(url) + return json.loads(body) if body else None + + +def visible_taxa(conn, minimum, shallow=SHALLOW_DEPTH): + """Taxa reachable through the columns the atlas draws, largest first. + + Two reasons to fetch an icon. Large groups get one because they are where + most assemblies are. The first few columns get one whatever their size, + because a group that borrows an ancestor's silhouette looks identical to its + siblings, and Ichthyosporea, Filasterea, Choanoflagellata and Rotosphaerida + all sit on the opening screen with single-digit assembly counts. + """ + rows = {r["taxid"]: dict(r) for r in conn.execute("SELECT taxid, parent_id, total_count FROM taxa")} + children = {} + for row in rows.values(): + if row["parent_id"] != row["taxid"]: + children.setdefault(row["parent_id"], []).append(row) + for group in children.values(): + group.sort(key=lambda r: (-r["total_count"], r["taxid"])) + seen, stack = set(), [EUKARYOTA] + while stack: + taxid = stack.pop() + if taxid in seen: + continue + seen.add(taxid) + stack.extend(child["taxid"] for child in children.get(taxid, [])[:COLUMN_LIMIT]) + near, level = {EUKARYOTA}, [EUKARYOTA] + for _ in range(shallow): + level = [c["taxid"] for t in level for c in children.get(t, [])[:COLUMN_LIMIT] if c["taxid"] not in near] + near.update(level) + chosen = [t for t in seen if rows[t]["total_count"] >= minimum or t in near] + return sorted(chosen, key=lambda t: -rows[t]["total_count"]) + + +def build(database, icon_dir, output, minimum=MIN_ASSEMBLIES, pause=0.1): + with sqlite3.connect(f"{Path(database).resolve().as_uri()}?mode=ro", uri=True) as conn: + conn.row_factory = sqlite3.Row + taxa = visible_taxa(conn, minimum) + # Listing endpoints reject a request that does not pin the catalogue build. + build_number = get_json(f"{API}/")["build"] + print(f"Resolving {len(taxa):,} taxa with at least {minimum} assemblies against build {build_number}", flush=True) + + nodes, shapes, images, assignments = {}, {}, {}, {} + counts = Counter() + for position, taxid in enumerate(taxa, 1): + resolved = get_json(f"{API}/resolve/ncbi.nlm.nih.gov/taxid/{taxid}?embed_primaryImage=true") + node = (resolved or {}).get("_links", {}).get("self", {}).get("href", "") + node = node.removeprefix("/nodes/").partition("?")[0] + if not node: + counts["unresolved"] += 1 + continue + if node not in nodes: + # Two things decide the pick. The node's own primary image is the one + # PhyloPic considers representative, so it gets a head start. But + # silhouettes range from 0.2 to 9.5 in aspect ratio, and anything far + # from square collapses into a sliver at icon size, so proportion is + # scored too and a badly shaped representative loses to a square one. + primary = (resolved.get("_embedded") or {}).get("primaryImage") or {} + candidates = [] + if primary: + candidates.append((candidate(primary), True)) + listing = get_json(f"{API}/images?build={build_number}&page=0&filter_clade={node}" + f"&filter_license_nc=false&filter_license_sa=false&embed_items=true") + candidates += [(candidate(item), False) for item in (listing or {}).get("_embedded", {}).get("items") or []] + usable = [(shape_score(found) - (PRIMARY_BONUS if is_primary else 0), found, is_primary) + for found, is_primary in candidates if found and is_free(found["license"])] + nodes[node] = "" + if usable: + _, best, is_primary = min(usable, key=lambda entry: entry[0]) + nodes[node] = best["uuid"] + shapes[best["uuid"]] = best["ratio"] + counts["primary_image" if is_primary else "clade_fallback"] += 1 + time.sleep(pause) + image = nodes[node] + if not image: + counts["no_free_image"] += 1 + continue + assignments[taxid] = image + counts["assigned"] += 1 + if position % 100 == 0: + print(f" {position:,}/{len(taxa):,} · {len(set(assignments.values())):,} distinct icons", flush=True) + time.sleep(pause) + + icon_dir = Path(icon_dir) + icon_dir.mkdir(parents=True, exist_ok=True) + keep = set() + for image in sorted(set(assignments.values())): + detail = get_json(f"{API}/images/{image}?build={build_number}") + links = (detail or {}).get("_links", {}) + vector = links.get("vectorFile", {}).get("href") + if not vector: + counts["no_vector"] += 1 + continue + target = icon_dir / f"{image}.svg" + if not target.exists(): + body = get(vector, headers={"User-Agent": HEADERS["User-Agent"]}) + if not body: + counts["download_failed"] += 1 + continue + target.write_bytes(body) + time.sleep(pause) + keep.add(image) + images[image] = {"license": links.get("license", {}).get("href"), + "attribution": detail.get("attribution"), + "contributor": links.get("contributor", {}).get("title"), + "page": f"https://www.phylopic.org/images/{image}", + "ratio": round(shapes.get(image, 1.0), 3), + "bytes": target.stat().st_size} + assignments = {t: i for t, i in assignments.items() if i in keep} + for stale in icon_dir.glob("*.svg"): + if stale.stem not in keep: + stale.unlink() + counts["removed"] += 1 + + licenses = Counter(meta["license"] for meta in images.values()) + unfree = sorted(license for license in licenses if not is_free(license)) + if unfree: + raise ValueError(f"Image with unusable licence slipped through: {unfree}") + payload = {"source": "https://www.phylopic.org", "build": build_number, + "api": f"{API}/resolve/ncbi.nlm.nih.gov/taxid/{{taxid}} then /images?filter_clade=…" + "&filter_license_nc=false&filter_license_sa=false", + "note": "Silhouettes are stored exactly as PhyloPic serves them, unmodified.", + "minimum_assemblies": minimum, + "counts": dict(counts, distinct_icons=len(images), bytes=sum(m["bytes"] for m in images.values())), + "licenses": dict(licenses), + "images": dict(sorted(images.items())), + "taxa": {str(t): assignments[t] for t in sorted(assignments)}} + Path(output).write_text(json.dumps(payload, indent=1)) + print(json.dumps({"counts": payload["counts"], "licenses": payload["licenses"]}, indent=2)) + + +def main(): + parser = argparse.ArgumentParser(description=__doc__) + parser.add_argument("--database", type=Path, default=ROOT / "data/taxonomy.sqlite") + parser.add_argument("--icon-dir", type=Path, default=ROOT / "data/icons") + parser.add_argument("--output", type=Path, default=ROOT / "data/icons.json") + parser.add_argument("--minimum", type=int, default=MIN_ASSEMBLIES) + args = parser.parse_args() + build(args.database, args.icon_dir, args.output, args.minimum) + + +if __name__ == "__main__": + main() diff --git a/taxonomy.py b/taxonomy.py index 78574d54b4324c8b0bd56b01f7aa5f66181dcbcb..45e99533339e8b1954fdbff52a894f781c094ce9 100644 --- a/taxonomy.py +++ b/taxonomy.py @@ -1,5 +1,7 @@ """Read-only taxonomy navigation, independent of the annotation lookup index.""" +from collections import Counter from contextlib import closing +import math from html import escape import json from pathlib import Path @@ -10,6 +12,14 @@ import gradio as gr ROOT = Path(__file__).resolve().parent DATABASE = ROOT / "data/taxonomy.sqlite" COMMON_NAMES = ROOT / "data/common_names.json" +ICONS = ROOT / "data/icons.json" +ICON_DIR = ROOT / "data/icons" +# Gradio serves whitelisted files from this route; see build_taxonomy_tab. +ICON_ROUTE = "/gradio_api/file=" +LICENSE_NAMES = {"https://creativecommons.org/publicdomain/zero/1.0/": "CC0 1.0", + "https://creativecommons.org/licenses/by/4.0/": "CC BY 4.0", + "https://creativecommons.org/licenses/by/3.0/": "CC BY 3.0", + "https://creativecommons.org/publicdomain/mark/1.0/": "Public Domain Mark 1.0"} EUKARYOTA = 2759 EUK_TREE = """WITH RECURSIVE euk(taxid) AS ( SELECT 2759 UNION ALL @@ -33,13 +43,21 @@ def encode_path(steps): class Taxonomy: - def __init__(self, path=DATABASE, common_names=COMMON_NAMES): + def __init__(self, path=DATABASE, common_names=COMMON_NAMES, icons=ICONS): self.path = Path(path) self.english, self.english_sources = {}, {} if Path(common_names).exists(): payload = json.loads(Path(common_names).read_text()) self.english = {int(t): name for t, name in payload["names"].items()} self.english_sources = payload.get("sources", {}) + self.icons, self.icon_credits, self.icon_meta = {}, {}, {} + if Path(icons).exists(): + payload = json.loads(Path(icons).read_text()) + self.icon_meta = {k: v for k, v in payload.items() if k not in ("images", "taxa")} + self.icon_credits = payload.get("images", {}) + self.icons = {int(t): image for t, image in payload.get("taxa", {}).items() + if (ICON_DIR / f"{image}.svg").exists()} + self._inherited_icons = {} with closing(self.connect()) as conn: self.metadata = json.loads(conn.execute("SELECT value FROM metadata").fetchone()[0]) self.eukaryote_ids = frozenset(r[0] for r in conn.execute(EUK_TREE + "SELECT taxid FROM euk")) @@ -63,6 +81,29 @@ class Taxonomy: rows = conn.execute(EUK_TREE + "SELECT taxa.* FROM taxa JOIN euk USING(taxid) WHERE name LIKE ? ESCAPE '\\' ORDER BY total_count DESC LIMIT 100", (pattern,)).fetchall() return [(f"{r['name']} · {r['total_count']:,} assemblies · taxid {r['taxid']}", str(r['taxid'])) for r in rows] + def icon_for(self, conn, taxid): + """Nearest icon at or above this taxon, following the lineage to Eukaryota. + + Returns the image and whether it belongs to this taxon or was borrowed. + """ + if taxid in self.icons: + return self.icons[taxid], False + if taxid in self._inherited_icons: + return self._inherited_icons[taxid], True + walked, current = [], taxid + for _ in range(MAX_DEPTH): + row = conn.execute("SELECT parent_id FROM taxa WHERE taxid=?", (current,)).fetchone() + if row is None or row['parent_id'] == current: + break + walked.append(current) + current = row['parent_id'] + if current in self.icons or current in self._inherited_icons: + break + found = self.icons.get(current) or self._inherited_icons.get(current, "") + for step in walked: + self._inherited_icons[step] = found + return found, True + def lineage(self, conn, taxid): rows = [dict(conn.execute("SELECT * FROM taxa WHERE taxid=?", (taxid,)).fetchone())] while rows[-1]['taxid'] != EUKARYOTA: @@ -96,11 +137,12 @@ class Taxonomy: def node(row, offset=0, **extra): return dict(taxid=row['taxid'], offset=offset, name=row['name'], label=row['name'], english=self.english.get(row['taxid'], ""), + **dict(zip(("icon", "borrowed_icon"), self.icon_for(conn, row['taxid']))), total=row['total_count'], covered=row.get('covered_total', 0), **extra) def remainder(rows, parent, start): return dict(taxid=parent, offset=start, name=f"Other lineages · {len(rows):,} groups (display aggregate)", - label=f"Other lineages ({len(rows):,})", english="", total=sum(r['total_count'] for r in rows), + label=f"Other lineages ({len(rows):,})", english="", icon="", borrowed_icon=False, total=sum(r['total_count'] for r in rows), covered=sum(r.get('covered_total', 0) for r in rows), aggregate=True) def column(step, selected): @@ -118,7 +160,7 @@ class Taxonomy: row = taxon(parent) if not offset and row['direct_count'] and rows: nodes.append(dict(taxid=parent, offset=0, name="Assemblies assigned directly to this taxon", - label="Direct assignments", english="", total=row['direct_count'], + label="Direct assignments", english="", icon="", borrowed_icon=False, total=row['direct_count'], covered=row.get('covered_direct', 0), direct=True)) return nodes @@ -143,7 +185,11 @@ class Taxonomy: return self.render(columns, steps, lineage, shortcuts, has_children=bool(tail)) def render(self, columns, steps, lineage, shortcuts, has_children): - top, chart, spacing, bar = 24, 460, 250, 14 + top, chart, spacing, bar = 24, 460, 274, 14 + # Silhouettes are not square: they run from tall and thin to long and + # flat. Fitting them all into one box turns most into slivers, so each + # gets its own box with the same area and its own proportions. + icon_area, icon_max, gutter = 23 * 23, 40, 46 width = max(830, 40 + (len(columns) - 1) * spacing + bar + 250) height = top * 2 + chart @@ -204,7 +250,10 @@ class Taxonomy: for depth, column in enumerate(columns): on_path = depth < len(steps) + shown = Counter(n['icon'] for n in column if n['icon']) for n in column: + if n['borrowed_icon'] and shown[n['icon']] > 1: + n['icon'] = "" # identical borrowed outlines read as "same group" x, y, h = n['x'], n['y'], n['h'] f = share(n) percent = 100 * f @@ -229,7 +278,17 @@ class Taxonomy: nodes.append(f'') label, english = clip(n['label'], MAX_LABEL), clip(n['english'], MAX_ENGLISH) stats = f"{percent:.1f}% · {n['covered']:,} / {n['total']:,}" if self.coverage else f"{n['total']:,} assemblies" - text_x = x + bar + 8 + # The gutter is reserved whether or not this node has a silhouette, so + # labels stay aligned down the column. + if n['icon']: + ratio = self.icon_credits.get(n['icon'], {}).get('ratio') or 1.0 + icon_h = min(icon_max, max(6, math.sqrt(icon_area / ratio))) + icon_w = min(icon_max, max(6, icon_h * ratio)) + icon_h = min(icon_max, max(6, icon_w / ratio)) + nodes.append(f'') + text_x = x + bar + 8 + gutter # Three lines when there is an English gloss, two without, both centred on the bar. head, stat_line = (cy - 10, cy + 16) if english else (cy - 3, cy + 13) nodes.append(f'{escape(label)}') @@ -285,12 +344,34 @@ class Taxonomy: ''' +def credit_lines(taxonomy): + """One line per artist, as CC BY asks, with the licences their images carry.""" + artists = {} + for image in set(taxonomy.icons.values()): + meta = taxonomy.icon_credits.get(image, {}) + name = meta.get("attribution") or meta.get("contributor") or "Unknown artist" + entry = artists.setdefault(name, {"licenses": set(), "pages": []}) + entry["licenses"].add(LICENSE_NAMES.get(meta.get("license"), meta.get("license") or "unknown licence")) + entry["pages"].append(meta.get("page")) + lines = [] + for name in sorted(artists, key=str.casefold): + entry = artists[name] + count = len(entry["pages"]) + lines.append(f"- [{name}]({entry['pages'][0]}) — {', '.join(sorted(entry['licenses']))}" + f"{f' — {count} silhouettes' if count > 1 else ''}") + return lines + + def build_taxonomy_tab(): """Render the tree and its controls inside the Genome atlas tab.""" if not DATABASE.exists(): gr.Markdown("The eukaryotic tree will appear when the taxonomy snapshot is available.") return taxonomy = Taxonomy() + if taxonomy.icons: + # The chart references each silhouette by URL, so the browser caches it + # once instead of the file riding along in every re-render. + gr.set_static_paths(paths=[ICON_DIR]) tree = gr.HTML(taxonomy.view(), css_template=(ROOT / "atlas.css").read_text(), js_on_load=(ROOT / "atlas.js").read_text(), apply_default_css=False, elem_id="eukaryotic-atlas") @@ -319,6 +400,11 @@ def build_taxonomy_tab(): matches.input(taxonomy_view, matches, tree) find.click(taxonomy_search, query, [matches, status]) query.submit(taxonomy_search, query, [matches, status]) + if taxonomy.icons: + with gr.Accordion("Silhouette credits", open=False, elem_classes="atlas-disclosure"): + gr.Markdown("\n".join(["Silhouettes from [PhyloPic](https://www.phylopic.org), used unmodified. " + "Public-domain images need no credit; the CC BY ones do, and every artist is listed here. " + "`data/icons.json` maps each taxon to its image.", ""] + credit_lines(taxonomy))) with gr.Accordion("About the tree and coverage", open=False, elem_classes="atlas-disclosure"): gr.Markdown("This tree follows **NCBI Taxonomy within Eukaryota**. Animals and fungi share the Opisthokonta branch; " "green plants include green algae. ‘Other lineages’ combines the remaining siblings for display and can be expanded. " @@ -335,8 +421,14 @@ def build_taxonomy_tab(): "Sources: [NCBI assembly summary](https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_genbank.txt), " "[NCBI Taxonomy](https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz) for both the tree and its common names, " "and [published annotations](https://huggingface.co/buckets/HuggingFaceBio/genbank-annotations).") + if taxonomy.icons: + gr.Markdown("Silhouettes come from [PhyloPic](https://www.phylopic.org), resolved from each taxon's NCBI ID and " + "stored unmodified. Only public-domain (CC0) and CC BY 4.0 images are used; NonCommercial and " + "ShareAlike images are filtered out at build time. A group without a silhouette of its own borrows " + "its nearest illustrated ancestor, so a fungal genus shows the fungal outline.") coverage = taxonomy.coverage or {} gr.JSON({"taxonomy_updated": taxonomy.metadata['created_at'], "coverage_updated": coverage.get('created_at'), + "silhouettes": taxonomy.icon_meta or None, "display_scope": "Eukaryota (NCBI taxid 2759) and its descendants only", "inventory_method": coverage.get('method'), "published_versions_outside_current_GenBank_snapshot": coverage.get('unmatched_assembly_versions'), diff --git a/tests/test_taxonomy.py b/tests/test_taxonomy.py index dd9ededd42d05d15f9bde34b3f927cdbf7732fda..17f2d29ccd89127f107e79133734a054e150b6e8 100644 --- a/tests/test_taxonomy.py +++ b/tests/test_taxonomy.py @@ -4,7 +4,7 @@ import sqlite3 import unittest from refresh_common_names import CURATED -from taxonomy import COMMON_NAMES, DATABASE, DEFAULT_PATH, MAX_ENGLISH, Taxonomy +from taxonomy import COMMON_NAMES, DATABASE, DEFAULT_PATH, ICON_DIR, ICONS, MAX_ENGLISH, Taxonomy @unittest.skipUnless(DATABASE.exists(), "taxonomy snapshot unavailable") @@ -64,6 +64,67 @@ class TaxonomyTests(unittest.TestCase): self.assertEqual({int(t) for t in names} & set(CURATED), set(CURATED) - redundant) self.assertEqual(names["6040"], "sponges") # straight from NCBI Taxonomy + def test_icons_are_free_to_use_and_present(self): + if not ICONS.exists(): + self.skipTest("silhouettes unavailable") + payload = json.loads(ICONS.read_text()) + self.assertTrue(payload["images"]) + for image, meta in payload["images"].items(): + # NonCommercial is legally murky for a company-run Space and ShareAlike + # would reach into the repository; refresh_icons.py filters both out. + self.assertNotIn("-nc", meta["license"], image) + self.assertNotIn("-sa", meta["license"], image) + self.assertTrue((ICON_DIR / f"{image}.svg").is_file(), image) + for taxid, image in payload["taxa"].items(): + self.assertIn(image, payload["images"], taxid) + + def test_small_groups_inherit_an_ancestor_icon(self): + if not self.taxonomy.icons: + self.skipTest("silhouettes unavailable") + with sqlite3.connect(f"{DATABASE.resolve().as_uri()}?mode=ro", uri=True) as conn: + conn.row_factory = sqlite3.Row + own, borrowed = self.taxonomy.icon_for(conn, 2759) + self.assertTrue(own) + self.assertFalse(borrowed) + # A taxon with no icon of its own still resolves, through its lineage. + uncovered = next(r['taxid'] for r in conn.execute( + "SELECT taxid FROM taxa WHERE total_count=1 ORDER BY taxid") + if r['taxid'] in self.taxonomy.eukaryote_ids and r['taxid'] not in self.taxonomy.icons) + image, borrowed = self.taxonomy.icon_for(conn, uncovered) + self.assertTrue(image) + self.assertTrue(borrowed) + self.assertTrue((ICON_DIR / f"{image}.svg").is_file()) + + def test_borrowed_icons_never_repeat_within_a_column(self): + if not self.taxonomy.icons: + self.skipTest("silhouettes unavailable") + for path in ("2759", DEFAULT_PATH, "2759/33154/33208", "2759/33154/33208/6072/33213"): + html = self.taxonomy.view(path) + # Columns are laid out left to right, so group the icons by their x. + drawn = re.findall(r']*?/data/icons/([0-9a-f-]+)\.svg"', html) + columns = {} + for x, image in drawn: + columns.setdefault(round(float(x)), []).append(image) + for x, images in columns.items(): + self.assertEqual(len(images), len(set(images)), f"{path} column at {x}") + + def test_chart_references_icons_by_url(self): + if not self.taxonomy.icons: + self.skipTest("silhouettes unavailable") + html = self.taxonomy.view(DEFAULT_PATH) + self.assertIn('class="tree-icon"', html) + for image in re.findall(r'href="[^"]*/data/icons/([0-9a-f-]+)\.svg"', html): + self.assertIn(image, self.taxonomy.icon_credits) + + def test_viewbox_spans_the_whole_chart(self): + # A stray local named width or height inside the node loop once shrank the + # viewBox to 23x23, which renders as a blank chart with every element intact. + for path in ("2759", DEFAULT_PATH, "2759/33154/33208"): + box = re.search(r'