replication-radar 0.3.3__tar.gz → 0.3.4__tar.gz

{replication_radar-0.3.3 → replication_radar-0.3.4}/DEMO.md

@@ -61,7 +61,7 @@ demo lands with just `replication-radar`.
 
 ---
 
-## 3 · The recording — two beats
+## 3 · The recording — three beats
 
 ### Beat 1 — the money shot: verify + cite (≈35 s)
 
@@ -81,7 +81,31 @@ confirmed, 1 qualifies it; here are the signed verdicts to cite,"* with links.
 "settled"; the MCP shows it's been checked 5 times and hands you **signed, citable verdicts** —
 including the one that *qualifies* it. That's the difference between paraphrasing and citing.
 
-### Beat 2 — the discovery side (≈20 s, optional)
+### Beat 2 — abstract → atomic claim → verdict: the two-project synergy (≈30 s)
+
+This is the strongest AI beat: the agent turns a paper's **text into a structured claim** and
+then **verifies** it, in one turn — your two hackathon projects composing (Jean's Hackaweek
+claim-*extraction* pipeline + the Radar's claim-*verification* layer). Needs the MCP **≥ 0.3.3**
+(it now returns the paper's abstract).
+
+**Type this prompt:**
+
+> Read the abstract of Soroye et al. 2020 (DOI 10.1126/science.aax8591), extract its single
+> central finding as one atomic AIDA sentence, and then tell me whether that exact claim has
+> been independently replicated.
+
+**What to expect:** the agent calls **`replication_status("10.1126/science.aax8591")`**, which now
+returns the **abstract** alongside the verdicts. The agent reads the abstract, **writes the atomic
+claim itself** (something like *"An increasing frequency of unusually hot days raises local
+extinction and lowers site occupancy of bumble bees, independent of land-use change"*), and then
+reports it has been **independently replicated 5× (4 confirm, 1 qualifies)** with the signed
+nanopubs.
+
+**The point to land:** *from a paper's text → a structured, atomic claim → a signed, citable
+verdict, in one turn.* Generation meets verification — the full "graph of verified knowledge" arc,
+live.
+
+### Beat 3 — the discovery side (≈20 s, optional)
 
 **Type this prompt:**
 

{replication_radar-0.3.3 → replication_radar-0.3.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: replication-radar
-Version: 0.3.3
+Version: 0.3.4
 Summary: MCP server that turns the OpenAIRE Graph into a ranked replication queue — impact-ranked targets and the Science Live verification overlay (retraction/supersession-aware).
 Project-URL: Homepage, https://github.com/ScienceLiveHub/replication-radar
 Project-URL: Repository, https://github.com/ScienceLiveHub/replication-radar

{replication_radar-0.3.3 → replication_radar-0.3.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "replication-radar"
-version = "0.3.3"
+version = "0.3.4"
 description = "MCP server that turns the OpenAIRE Graph into a ranked replication queue — impact-ranked targets and the Science Live verification overlay (retraction/supersession-aware)."
 readme = "README.md"
 requires-python = ">=3.10"

{replication_radar-0.3.3 → replication_radar-0.3.4}/site/app.js

@@ -122,6 +122,12 @@ const outcomeLinks = (outs) => {
   return ` · ${lead} ` + outs.map((o) =>
     `<a class="onp ${verdictClass(o.verdict)}" href="${o.np}" target="_blank" rel="noopener" title="${esc(o.verdict)} — open the signed nanopub">${verdictLabel(o.verdict)}</a>`).join(" ");
 };
+// "See all replications" → the Science Live constellation page: every signed replication of this
+// paper's claims, grouped by claim, with each verdict + the full chain. (Switch the host to
+// platform.sciencelive4all.org once the page is deployed to prod.)
+const CONSTELLATION = "https://platform-dev.sciencelive4all.org/np/replications?doi=";
+const constellationLink = (doi, n) => !doi ? "" :
+  ` · <a class="seeall" href="${CONSTELLATION}${encodeURIComponent(doi)}" target="_blank" rel="noopener">see ${n === 1 ? "the replication" : `all ${n} replications`} →</a>`;
 // Agreement pattern across the independent replication verdicts — many-agree ≠ disagree.
 const agreementOf = (doi) => {
   const vs = outcomesFor(doi).map((o) => o.verdict);
@@ -188,6 +194,15 @@ const subjectsOf = (rec, scheme) => [...new Set((rec.subjects || []).filter((s)
 const cleanFos = (arr) => [...new Set(arr.map((v) => v.replace(/^\d+\s+/, "")).filter((v) => v && !/^\d+$/.test(v)))];
 const oaOf = (rec) => rec.openAccessColor || ((rec.bestAccessRight || {}).label || "").toLowerCase();
 const urlOf = (rec) => (rec.instances && rec.instances[0] && rec.instances[0].urls && rec.instances[0].urls[0]) || null;
+// Paper abstract from OpenAIRE `descriptions` — strip JATS/HTML tags, decode entities, collapse
+// whitespace (mirrors the Python _abstract). Gives an OPEN target the context of what it claims.
+const abstractOf = (rec) => {
+  let t = (rec.descriptions || []).filter((d) => typeof d === "string").join(" ");
+  if (!t) return "";
+  t = t.replace(/<[^>]+>/g, " ");
+  const d = document.createElement("textarea"); d.innerHTML = t; t = d.value;   // decode entities
+  return t.replace(/\s+/g, " ").trim().replace(/^abstract[\s:.\-–—]*/i, "");    // drop redundant "Abstract" prefix
+};
 
 // ---------- software FAIR + usage assessment (grounded, live from GitHub + SWH) ----------
 // Computes the fair-software.eu 5 recommendations + usage from authoritative sources
@@ -371,7 +386,7 @@ async function loadCurated() {
     if (rec) {
       c.title = rec.mainTitle || doi; c.citations = impact(rec).citationCount || 0;
       c.cls = impact(rec).citationClass; c.infl = impact(rec).influenceClass;
-      c.impl = impact(rec).impulseClass; c.year = yearOf(rec);
+      c.impl = impact(rec).impulseClass; c.year = yearOf(rec); c.abstract = abstractOf(rec);
     } else { c.title = c.title || doi; }
   }));
 }
@@ -412,6 +427,7 @@ async function radar(topic) {
     const readiness = readinessFrom(mat.score, impactScore, momentum);   // computed for ALL (incl. verified)
     return {
       title: p.mainTitle || "", doi, citations: impact(p).citationCount || 0,
+      abstract: abstractOf(p),
       cls: impact(p).citationClass, infl: impact(p).influenceClass,
       year: yearOf(p), impl: impact(p).impulseClass || null,
       mat, parts: { mat: mat.score, impact: impactScore, momentum },
@@ -490,7 +506,7 @@ async function radar(topic) {
     const matScore = c.state === "rocrate" ? 1.0 : 0.6;
     targets.push({
       title: c.title, doi, citations: c.citations || 0, cls: c.cls, infl: c.infl,
-      year: c.year || null, impl: c.impl || null,
+      year: c.year || null, impl: c.impl || null, abstract: c.abstract || "",
       mat: { score: matScore, state: c.state, code: c.code || null, resolved: true, data: c.data || [], source: c.source || "the paper", lang: c.lang },
       parts: { mat: matScore, impact: impactScore, momentum },
       status: VERDICTS[doi] ? "VERIFIED" : "OPEN",
@@ -519,6 +535,36 @@ const esc = (s) => (s || "").replace(/[&<>]/g, (c) => ({ "&": "&amp;", "<": "&lt
 const PER_PAGE = 10;
 let _targets = [], _tpage = 0, _tfilter = new Set();
 
+// FAIR-software block: a fold that expands to the 5 fair-software.eu recommendations (met/missing),
+// with a live Software Heritage link (browse the archived snapshot, or Save Code Now if not yet).
+const FAIR_REC = { repository: "public repository", license: "open licence", registry: "in a registry", citation: "citable (CITATION.cff / DOI)", quality: "quality artefacts" };
+// Software Heritage status: archived → browse the snapshot; not yet → a one-click "archive it"
+// button that POSTs to the SWH Save-Code-Now API (anonymous, CORS-open, no account needed).
+const swhHtml = (repo, archived) => {
+  if (archived) {
+    const b = repo ? `https://archive.softwareheritage.org/browse/origin/directory/?origin_url=${encodeURIComponent(repo)}` : null;
+    return b ? `<a class="swhok" href="${b}" target="_blank" rel="noopener" title="Browse the archived snapshot in Software Heritage">in Software Heritage</a>` : `<span class="swhok">in Software Heritage</span>`;
+  }
+  if (!repo) return `<a class="swhno" href="https://archive.softwareheritage.org/save/" target="_blank" rel="noopener">not yet archived</a>`;
+  return `<button type="button" class="swhsave" data-repo="${esc(repo)}" onclick="swhSave(this)" title="Open Software Heritage Save Code Now and copy this repo's URL ready to paste">not yet archived — archive it →</button>`;
+};
+// SWH's save API can't be called cross-origin from a static page (the repo URL sits in the request
+// path and the form can't be pre-filled), so do the reliable thing: copy the repo URL to the
+// clipboard and open the Save Code Now form — one click, then paste (Cmd/Ctrl-V) and submit.
+window.swhSave = async (btn) => {
+  const repo = btn.dataset.repo || "";
+  try { if (repo && navigator.clipboard) { await navigator.clipboard.writeText(repo); btn.classList.add("done"); btn.innerHTML = `${ICON.check}repo URL copied — paste it into the form`; } }
+  catch (e) { /* clipboard blocked — the form still opens */ }
+  window.open("https://archive.softwareheritage.org/save/", "_blank", "noopener");
+};
+function fairBlock(f, repo) {
+  const recs = Object.entries(f.recs || {}).map(([k, ok]) =>
+    `<span class="${ok ? "rok" : "rno"}">${ok ? ICON.check : ICON.x}${FAIR_REC[k] || k}</span>`).join("");
+  // stop the SWH link's click from toggling the fold
+  const swh = ` · <span onclick="event.stopPropagation()">${swhHtml(repo, f.swh)}</span>`;
+  return `<details class="tfair"><summary>FAIR software <b>${f.score}/5</b> · ${ICON.star}${f.stars}${swh}</summary><div class="fairrecs">${recs}</div></details>`;
+}
+
 function targetRow(t) {
   const p = t.parts || {};
   const scoreTitle = t.status === "VERIFIED"
@@ -543,22 +589,27 @@ function targetRow(t) {
   const cl = t.status === "VERIFIED" ? claimFor(t.outcome_np) : null;
   const claimLine = (cl && (cl.aida || cl.label))
     ? `<div class="tclaim"><span class="claimlbl">claim:</span> <span class="claimq">“${esc(cl.aida || cl.label)}”</span>${cl.type ? ` <span class="badge ctype" title="FORRT claim type">${esc(cl.type)}</span>` : ""}</div>` : "";
+  // OPEN targets have no verdict-chain claim yet — show the abstract for context on what you'd
+  // test. Long ones fold (click to expand the full text) so the card stays compact.
+  const absLine = (t.status !== "VERIFIED" && t.abstract)
+    ? (t.abstract.length <= 240
+        ? `<div class="tabstract"><span class="claimlbl">abstract</span> ${esc(t.abstract)}</div>`
+        : `<details class="tabstract"><summary><span class="claimlbl">abstract</span> <span class="absnip">${esc(t.abstract.slice(0, 200))}…</span></summary><div class="absfull">${esc(t.abstract)}</div></details>`)
+    : "";
   const outs = t.status === "VERIFIED" ? outcomesFor(t.doi).filter((o) => o.np) : [];
   const verdictLink = (t.status === "VERIFIED")
-    ? `<div class="tverdict">independently checked by <a href="https://sciencelive4all.org" target="_blank" rel="noopener">Science Live</a> — <b>${esc(agreementOf(t.doi).why)}</b>${outcomeLinks(outs)}</div>` : "";
+    ? `<div class="tverdict">independently checked by <a href="https://sciencelive4all.org" target="_blank" rel="noopener">Science Live</a> — <b>${esc(agreementOf(t.doi).why)}</b>${constellationLink(t.doi, outs.length)}</div>` : "";
   const resolvedNote = (t.mat && t.mat.resolved)
     ? `<div class="tresolved">↳ materials resolved from ${esc(t.mat.source || "the paper")} (not in OpenAIRE): <a href="${esc(t.mat.code || "")}" target="_blank" rel="noopener">code repo</a>${(t.mat.data && t.mat.data.length) ? ` · data: ${t.mat.data.map(esc).join(", ")}` : ""}</div>`
     : "";
-  const fairNote = t.fair
-    ? `<div class="tfair">FAIR software <b>${t.fair.score}/5</b> · ${ICON.star}${t.fair.stars}${t.fair.swh ? " · in Software Heritage" : ""}</div>`
-    : "";
+  const fairNote = t.fair ? fairBlock(t.fair, t.mat && t.mat.code) : "";
   // OPEN targets get a next step: discovery here → the FORRT template handles the nanopub chain.
   const replicateCTA = (t.status !== "VERIFIED")
     ? `<div class="treplicate"><a href="https://github.com/ScienceLiveHub/forrt-replication-template" target="_blank" rel="noopener" title="Start a replication from the FORRT template — it scaffolds the repo and the signed nanopub chain (Claim · Study · Outcome)">▷ Replicate this with the template →</a></div>`
     : "";
   return `<div class="target ${t.status === "VERIFIED" ? "verified" : ""}">
     ${score}
-    <div class="t-main">${badge}<br><b>${esc(t.title)}</b>${meta}${claimLine}${verdictLink}${resolvedNote}${fairNote}${replicateCTA}</div>
+    <div class="t-main">${badge}<br><b>${esc(t.title)}</b>${meta}${claimLine}${absLine}${verdictLink}${resolvedNote}${fairNote}${replicateCTA}</div>
     <div class="t-right">${t.citations.toLocaleString()} cites<br>${link}</div>
   </div>`;
 }
@@ -623,8 +674,8 @@ function renderVerified(inField) {
     if (v.repl) {
       const f = v.repl.fair;
       const fairBadge = f
-        ? `<div class="fairrecs"><b>FAIR software (${f.score}/5):</b> ${Object.entries(f.recs).map(([k, ok]) => `<span class="${ok ? "rok" : "rno"}">${ok ? ICON.check : ICON.x}${k}</span>`).join("")}</div>
-        <div class="fairline">${ICON.star}${f.stars} stars · ${ICON.fork}${f.forks} forks · ${f.swh ? `<span class="swhok">in Software Heritage</span>` : `<span class="swhno">not yet in Software Heritage</span>`}</div>`
+        ? `<div class="fairrecs"><b>FAIR software (${f.score}/5):</b> ${Object.entries(f.recs).map(([k, ok]) => `<span class="${ok ? "rok" : "rno"}">${ok ? ICON.check : ICON.x}${FAIR_REC[k] || k}</span>`).join("")}</div>
+        <div class="fairline">${ICON.star}${f.stars} stars · ${ICON.fork}${f.forks} forks · ${swhHtml(v.repl.code, f.swh)}</div>`
         : "";
       const nodeHref = v.repl.code && v.repl.code.includes("github") ? v.repl.code : v.repl.url;
       repl = `<div class="vrepl">↳ replication is an OpenAIRE node: <a href="${nodeHref}" target="_blank" rel="noopener">${esc(v.repl.title).slice(0, 44) || v.repl.doi}</a> <span class="ochip type">${esc(v.repl.type)}</span></div>${fairBadge}`;
@@ -640,7 +691,7 @@ function renderVerified(inField) {
       <span class="vt">${esc(v.title).slice(0, 82)}</span>
       <div class="ochips">${chips}</div>
       ${vClaimLine}
-      <div class="vline"><span class="vv ${partialOf(v) ? "partial" : ""}">${v.verdicts.join(", ")}</span> — independently checked by <a href="https://sciencelive4all.org" target="_blank" rel="noopener">Science Live</a> ${vouts.length ? outcomeLinks(vouts) : (v.cito_np ? `· <a href="${v.cito_np}" target="_blank" rel="noopener">verdict chain →</a>` : "")}</div>
+      <div class="vline"><span class="vv ${partialOf(v) ? "partial" : ""}">${v.verdicts.join(", ")}</span> — independently checked by <a href="https://sciencelive4all.org" target="_blank" rel="noopener">Science Live</a> ${vouts.length ? constellationLink(v.doi, vouts.length) : (v.cito_np ? `· <a href="${v.cito_np}" target="_blank" rel="noopener">verdict chain →</a>` : "")}</div>
       ${repl}
     </li>`;
   };

{replication_radar-0.3.3 → replication_radar-0.3.4}/site/style.css

@@ -98,10 +98,19 @@ header .sub{margin:0;color:#aebfdc;font-size:14px}
 .badge .ic{margin-right:3px}
 .tfair .ic,.fairline .ic,.fairrecs .ic{margin-right:2px}
 .tclaim{font-size:12.5px;color:var(--ink);margin-top:6px;line-height:1.5}
+.tabstract{font-size:12px;color:var(--mut);margin-top:6px;line-height:1.5}
+.tabstract .claimlbl{color:var(--navy2)}
+details.tabstract > summary{cursor:pointer;list-style:none}
+details.tabstract > summary::-webkit-details-marker{display:none}
+details.tabstract > summary::after{content:" ▸ more";color:var(--magenta);font-weight:600;font-size:11px}
+details.tabstract[open] > summary::after{content:" ▾ less"}
+details.tabstract[open] .absnip{display:none}
+details.tabstract .absfull{margin-top:3px}
 .claimlbl{font-size:10px;font-weight:700;text-transform:uppercase;letter-spacing:.4px;color:var(--green)}
 .claimq{font-style:italic}
 .badge.ctype{background:#e7edf6;color:var(--navy2);text-transform:capitalize}
 .tverdict{font-size:12px;color:var(--mut);margin-top:4px}
+.seeall{font-weight:600}
 .onp{display:inline-block;min-width:18px;text-align:center;border:1px solid var(--line);border-radius:4px;padding:0 6px;margin:0 2px;font-weight:700;font-size:11px;line-height:1.6}
 .onp:hover{text-decoration:none}
 /* white body so the chip is visible on tinted (verified) cards; verdict lives in border+text+hover */
@@ -116,6 +125,11 @@ header .sub{margin:0;color:#aebfdc;font-size:14px}
 .tresolved a{font-weight:600}
 .tfair{font-size:12px;color:var(--mut);margin-top:3px}
 .tfair b{color:var(--navy2)}
+details.tfair > summary{cursor:pointer;list-style:none}
+details.tfair > summary::-webkit-details-marker{display:none}
+details.tfair > summary::after{content:" ▸";color:var(--navy2)}
+details.tfair[open] > summary::after{content:" ▾"}
+details.tfair .fairrecs{margin-top:5px}
 .treplicate{margin-top:7px}
 .treplicate a{font-size:12px;font-weight:700;background:var(--magenta-soft);color:#a32a6a;padding:4px 11px;border-radius:7px;display:inline-block}
 .treplicate a:hover{background:var(--magenta);color:#fff;text-decoration:none}
@@ -154,6 +168,11 @@ header .sub{margin:0;color:#aebfdc;font-size:14px}
 .fairbar i{display:block;height:100%;background:var(--green)}
 .swhok{color:var(--green);font-weight:600}
 .swhno{color:#8a5804}
+.swhsave{background:none;border:0;padding:0;margin:0;font:inherit;font-weight:600;color:#8a5804;cursor:pointer;text-decoration:underline}
+.swhsave:hover:not(:disabled){color:#6f560f}
+.swhsave:disabled{cursor:default;text-decoration:none}
+.swhsave.done{color:var(--green);text-decoration:none}
+.swhsave .ic{margin-right:3px}
 .ochip.wait{background:#fdecc8;color:#8a5804}
 .vnone{color:#a32a6a;background:var(--magenta-soft);padding:12px 14px;border-radius:8px;font-size:13.5px}
 .vmore-stat{margin-top:14px;padding-top:12px;border-top:1px solid var(--line);font-size:12.5px;color:var(--mut)}