dbtips-curate 0.2.0__py3-none-any.whl

dbtips_curate/__init__.py

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+__version__ = "0.2.0"

dbtips_curate/cli/_common.py

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+"""Helpers shared by command handlers — config + entity resolution."""
+
+from __future__ import annotations
+
+import sys
+from pathlib import Path
+
+import typer
+
+from dbtips_curate.cli._output import emit_error
+from dbtips_curate.core.config import Config, load_config
+from dbtips_curate.core.fs import EntityPaths
+from dbtips_curate.core.schema import Section
+
+# Sentinel: when a section-aware command's --type option receives this,
+# resolve() derives entity_type from the section's entity_scope. Explicit
+# --type values on the CLI still win — this only fires when the user doesn't
+# pass --type. Used by every command that also takes --section (delete, add,
+# patch, entity status/track/snapshot/records/diff/ingest/compare/finalize).
+AUTO_ENTITY_TYPE = "__auto__"
+
+# Back-compat default for commands that DON'T take --section (list, undo).
+# They can't consult the section registry to auto-derive the type.
+DEFAULT_ENTITY_TYPE = "target_disease"
+DEFAULT_SECTION = "/evidence/target-literature/"
+
+
+def get_config(ctx: typer.Context) -> Config:
+    config = ctx.obj.get("config") if ctx.obj else None
+    if config is None:
+        try:
+            config = load_config()
+        except FileNotFoundError as e:
+            emit_error("NO_CONFIG", str(e), json_mode=ctx.obj.get("json", False),
+                       hint="Run from inside a directory under your platform repo "
+                            "with a curation/.dbtips-curate.toml")
+            raise typer.Exit(code=2)
+        ctx.ensure_object(dict)
+        ctx.obj["config"] = config
+    return config
+
+
+def resolve(ctx: typer.Context, entity_type: str, entity_id: str, endpoint: str) -> tuple[EntityPaths, Section]:
+    config = get_config(ctx)
+    try:
+        section = config.registry.get(endpoint)
+    except KeyError:
+        emit_error("UNKNOWN_SECTION", f"No schema registered for section {endpoint!r}",
+                   json_mode=ctx.obj.get("json", False),
+                   hint="Add an entry under [sections.\"%s\"] in .dbtips-curate.toml" % endpoint)
+        raise typer.Exit(code=2)
+    # Derive --type from the section's entity_scope when the user didn't pass
+    # --type explicitly. Explicit --type still wins (needed for tests and for
+    # sections that are legitimately curated in both scopes).
+    if entity_type == AUTO_ENTITY_TYPE:
+        entity_type = section.entity_scope
+    paths = EntityPaths(config, entity_type, entity_id)
+    return paths, section
+
+
+def require_served_file(ctx: typer.Context, paths: EntityPaths) -> None:
+    if not paths.served_path.exists():
+        emit_error("NO_SERVED_FILE",
+                   f"Served file not found: {paths.served_path}",
+                   json_mode=ctx.obj.get("json", False),
+                   hint="Has the pipeline generated this entity yet?")
+        raise typer.Exit(code=1)

dbtips_curate/cli/_output.py

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+"""Shared output helpers — keeps human/JSON formatting out of command handlers."""
+
+from __future__ import annotations
+
+import json
+import os
+import sys
+from typing import Any
+
+from rich.console import Console
+
+
+def _stdout() -> Console:
+    return Console(file=sys.stdout, force_terminal=False, no_color=_no_color())
+
+
+def _stderr() -> Console:
+    return Console(file=sys.stderr, force_terminal=False, no_color=_no_color())
+
+
+def _no_color() -> bool:
+    return bool(os.environ.get("NO_COLOR")) or not sys.stdout.isatty()
+
+
+def emit_ok(data: Any, *, json_mode: bool, human: str | None = None) -> None:
+    """Result -> stdout. JSON or human."""
+    if json_mode:
+        print(json.dumps({"ok": True, "data": data}, default=str))
+    else:
+        if human is not None:
+            print(human)
+        else:
+            print(json.dumps(data, indent=2, default=str))
+
+
+def emit_error(code: str, message: str, *, json_mode: bool, hint: str | None = None) -> None:
+    """Errors -> stderr; do not pollute stdout."""
+    if json_mode:
+        payload = {"ok": False, "error": {"code": code, "message": message}}
+        if hint:
+            payload["error"]["hint"] = hint
+        print(json.dumps(payload), file=sys.stderr)
+    else:
+        print(f"Error: {message}", file=sys.stderr)
+        if hint:
+            print(f"  {hint}", file=sys.stderr)
+
+
+def emit_progress(message: str) -> None:
+    """Progress -> stderr in both modes."""
+    print(message, file=sys.stderr)

dbtips_curate/cli/_widget.py

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+"""Self-contained HTML artifact generator for the diff preview.
+
+The CLI reads the cache directly, so it can inline *full* abstracts for every
+record with no token budget — unlike a chat agent that has to transcribe the
+widget code through its own context. `render_diff_widget` returns a widget
+fragment (no <html>/<head>/<body>) suitable for inline artifact rendering in
+the Claude Code desktop app: CSS variables for theming, a shared <dialog>
+abstract modal, pagination, checkbox selection, and `sendPrompt` action
+buttons that the dbtips-curate skill's batch-execution rule picks up.
+"""
+
+from __future__ import annotations
+
+import json
+from typing import Any
+
+
+def _rows_from_queue(entries: list[dict], identity_key: str) -> list[dict]:
+    """Flatten a diff queue into rows the widget understands."""
+    rows = []
+    for e in entries:
+        preview = e.get("_preview", {}) or {}
+        identity = {k: v for k, v in e.items() if k != "_preview"}
+        pmid = identity.get(identity_key)
+        if pmid is None and identity:
+            pmid = next(iter(identity.values()))
+        # Display title falls back across sections: literature Title, reagent
+        # product_name, pathway figtitle, assay Description. The modal body uses
+        # the richest text available (Abstract / description).
+        title = (preview.get("Title") or preview.get("product_name")
+                 or preview.get("figtitle") or preview.get("Description") or "")
+        provider = preview.get("Provider")
+        if provider and not preview.get("Title"):
+            title = f"{title} — {provider}"
+        rows.append({
+            "pmid": str(pmid) if pmid is not None else "",
+            "year": preview.get("Year"),
+            "cite": preview.get("citedby"),
+            "title": title,
+            "abstract": preview.get("Abstract") or preview.get("description") or "",
+        })
+    return rows
+
+
+def render_diff_widget(payload: dict[str, Any], *, identity_key: str = "PMID") -> str:
+    """Build the inline diff artifact for `entity diff --emit-widget`."""
+    entity_id = payload["entity"]
+    queue = payload.get("queue", {})
+    totals = payload.get("totals", {})
+
+    data = {
+        "entity": entity_id,
+        "base_raw": payload.get("base_raw"),
+        "section": payload.get("section"),
+        "totals": totals,
+        "new": _rows_from_queue(queue.get("new", []), identity_key),
+        "removed": _rows_from_queue(queue.get("removed_by_pipeline", []), identity_key),
+        "resurrected": _rows_from_queue(queue.get("resurrected", []), identity_key),
+        "conflicts": queue.get("conflicts", []),
+    }
+    data_json = json.dumps(data, ensure_ascii=False, default=str)
+    # Close any stray </script> inside abstracts so the embed can't break out.
+    data_json = data_json.replace("</", "<\\/")
+    return _TEMPLATE.replace("/*__DATA__*/", data_json)
+
+
+_TEMPLATE = r"""<div style="padding:0.5rem 0;">
+<h2 class="sr-only">Diff preview artifact: new, removed-by-pipeline, resurrected, and conflict records with full-abstract modal, pagination, and batch actions.</h2>
+<div id="summary" style="font-size:13px; color:var(--color-text-secondary); margin-bottom:14px;"></div>
+
+<div style="display:flex; gap:6px; margin-bottom:12px; flex-wrap:wrap;">
+  <button class="tab" data-tab="new">New from pipeline</button>
+  <button class="tab" data-tab="removed">Removed by pipeline</button>
+  <button class="tab" data-tab="resurrected">Resurrected</button>
+  <button class="tab" data-tab="conflicts">Conflicts</button>
+</div>
+
+<div id="toolbar" style="display:flex; gap:8px; flex-wrap:wrap; align-items:center; margin-bottom:10px;">
+  <span id="secnote" style="font-size:12px; color:var(--color-text-tertiary); flex:1;"></span>
+  <button id="checkall" style="font-size:13px;">Select all on page</button>
+  <button id="clearall" style="font-size:13px;">Clear</button>
+</div>
+
+<table style="width:100%; border-collapse:collapse; font-size:13px; table-layout:fixed;">
+  <colgroup><col style="width:30px"><col style="width:26px"><col style="width:78px"><col style="width:52px"><col style="width:42px"><col><col style="width:54px"></colgroup>
+  <thead><tr id="thead" style="text-align:left; color:var(--color-text-secondary); border-bottom:0.5px solid var(--color-border-secondary);"></tr></thead>
+  <tbody id="rows"></tbody>
+</table>
+
+<div style="display:flex; gap:8px; align-items:center; justify-content:center; margin-top:14px;">
+  <button id="prev" style="font-size:13px;"><i class="ti ti-chevron-left" aria-hidden="true"></i> Prev</button>
+  <span id="pageinfo" style="font-size:13px; color:var(--color-text-secondary); min-width:130px; text-align:center;"></span>
+  <button id="next" style="font-size:13px;">Next <i class="ti ti-chevron-right" aria-hidden="true"></i></button>
+</div>
+
+<div style="border-top:0.5px solid var(--color-border-tertiary); margin-top:16px; padding-top:14px; display:flex; align-items:center; gap:12px;">
+  <span id="selsum" style="font-size:13px; color:var(--color-text-secondary); flex:1;"></span>
+  <button id="apply" style="font-size:14px; padding:7px 18px; color:var(--color-text-danger); border-color:var(--color-border-danger);"><i class="ti ti-trash" aria-hidden="true"></i> Apply <span id="applyverb">deletions</span> &#8599;</button>
+</div>
+
+<dialog id="amodal" style="max-width:620px; padding:18px; border:none; border-radius:var(--border-radius-lg); background:var(--color-background-primary); color:var(--color-text-primary);">
+  <header style="display:flex; align-items:center; gap:8px; margin-bottom:10px;">
+    <strong id="m-pmid" style="font-family:var(--font-mono); font-size:13px;"></strong>
+    <span style="flex:1"></span>
+    <button onclick="document.getElementById('amodal').close()" style="font-size:13px;">Close</button>
+  </header>
+  <p id="m-title" style="font-size:14px; font-weight:500; margin:0 0 10px; line-height:1.4;"></p>
+  <p id="m-abs" style="white-space:pre-wrap; line-height:1.55; font-size:13px; color:var(--color-text-secondary); max-height:55vh; overflow:auto; margin:0;"></p>
+</dialog>
+</div>
+<style>
+.tab{font-size:13px;}
+.tab[aria-selected="true"]{background:var(--color-background-secondary); border-color:var(--color-border-primary);}
+</style>
+<script>
+const DB=/*__DATA__*/;
+const PS=20;
+const VERB={new:"deletions", removed:"drops"};
+const ACTION={
+  new:(ids)=>`Delete these ${ids.length} new-from-pipeline records for ${DB.entity} (run op delete on each, no further confirmation needed): ${ids.join(", ")}`,
+  removed:(ids)=>`Delete these ${ids.length} removed-by-pipeline records for ${DB.entity} (run op delete on each, no further confirmation needed): ${ids.join(", ")}`
+};
+let tab="new", page=0;
+const sel={new:new Set(), removed:new Set()};
+function esc(s){return String(s==null?"":s).replace(/&/g,"&amp;").replace(/</g,"&lt;");}
+function fmt(v){return v==null?"":v;}
+function curRows(){
+  if(tab==="new")return DB.new;
+  if(tab==="removed")return DB.removed;
+  if(tab==="resurrected")return DB.resurrected;
+  return DB.conflicts;
+}
+function summary(){
+  const t=DB.totals||{};
+  document.getElementById("summary").innerHTML=
+    `<strong>${esc(DB.entity)}</strong> &middot; base=${esc(DB.base_raw||"—")} vs current served &middot; `+
+    `merged ${fmt(t.merged)} &middot; new ${fmt(t.new_from_pipeline)} &middot; removed ${fmt(t.removed_by_pipeline)} &middot; `+
+    `resurrected ${fmt(t.resurrected_tombstones)} &middot; conflicts ${fmt(t.conflicts)}`;
+  const selectable=(tab==="new"||tab==="removed");
+  document.getElementById("apply").style.display=selectable?"":"none";
+  document.getElementById("checkall").style.display=selectable?"":"none";
+  document.getElementById("clearall").style.display=selectable?"":"none";
+  document.getElementById("applyverb").textContent=VERB[tab]||"";
+  const n=selectable?sel[tab].size:0;
+  document.getElementById("selsum").textContent=n?`${n} selected`:"No records selected";
+  document.getElementById("apply").disabled=n===0;
+  const notes={new:"Records the refresh newly emitted — triage and delete noise.",
+    removed:"In the previous file but dropped by the refresh — retained on ingest unless you drop them.",
+    resurrected:"You deleted these before; the pipeline re-emitted them. They stay deleted on ingest.",
+    conflicts:"Field-level disagreements between your patch and the pipeline."};
+  document.getElementById("secnote").textContent=notes[tab]||"";
+}
+function openModal(r){
+  document.getElementById("m-pmid").textContent="PMID "+r.pmid+(r.year?" · "+r.year:"")+(r.cite!=null?" · cited "+r.cite:"");
+  document.getElementById("m-title").textContent=r.title||"";
+  document.getElementById("m-abs").textContent=r.abstract||"(no abstract)";
+  document.getElementById("amodal").showModal();
+}
+function render(){
+  document.querySelectorAll(".tab").forEach(b=>b.setAttribute("aria-selected", b.dataset.tab===tab?"true":"false"));
+  const rows=curRows();
+  const TP=Math.max(1, Math.ceil(rows.length/PS));
+  if(page>=TP)page=0;
+  const thead=document.getElementById("thead");
+  const tb=document.getElementById("rows"); tb.innerHTML="";
+  if(tab==="conflicts"){
+    thead.innerHTML=`<th style="padding:8px 4px;">key</th><th>field</th><th>ours</th><th>theirs</th><th>base</th>`;
+    rows.slice(page*PS,page*PS+PS).forEach(c=>{
+      const tr=document.createElement("tr"); tr.style.borderTop="0.5px solid var(--color-border-tertiary)";
+      tr.innerHTML=`<td style="padding:8px 4px; font-family:var(--font-mono); font-size:12px;">${esc(JSON.stringify(c.key))}</td>`+
+        `<td>${esc(c.field)}</td><td>${esc(c.ours)}</td><td>${esc(c.theirs)}</td><td>${esc(c.base)}</td>`;
+      tb.appendChild(tr);
+    });
+  } else {
+    const selectable=(tab==="new"||tab==="removed");
+    thead.innerHTML=`<th style="padding:8px 4px;">${selectable?'<i class="ti ti-trash" aria-hidden="true"></i>':''}</th><th>#</th><th>PMID</th><th>Year</th><th>Cite</th><th>Title</th><th>Abs</th>`;
+    const start=page*PS, end=Math.min(start+PS, rows.length);
+    for(let i=start;i<end;i++){
+      const r=rows[i];
+      const tr=document.createElement("tr"); tr.style.borderTop="0.5px solid var(--color-border-tertiary)";
+      const box=selectable?`<input type="checkbox" data-pmid="${esc(r.pmid)}" ${sel[tab].has(r.pmid)?"checked":""} style="width:16px;height:16px;cursor:pointer;">`:"";
+      tr.innerHTML=`<td style="padding:9px 4px; vertical-align:top;">${box}</td>`+
+        `<td style="vertical-align:top; color:var(--color-text-tertiary);">${i+1}</td>`+
+        `<td style="vertical-align:top; font-family:var(--font-mono); font-size:12px;">${esc(r.pmid)}</td>`+
+        `<td style="vertical-align:top;">${esc(fmt(r.year))}</td>`+
+        `<td style="vertical-align:top;">${esc(fmt(r.cite))}</td>`+
+        `<td style="vertical-align:top; white-space:normal; word-break:break-word; line-height:1.45;">${esc(r.title)}</td>`+
+        `<td style="vertical-align:top;"><button data-i="${i}" class="absbtn" style="font-size:11px; padding:3px 8px;"><i class="ti ti-file-text" aria-hidden="true"></i></button></td>`;
+      tb.appendChild(tr);
+    }
+    tb.querySelectorAll("input[type=checkbox]").forEach(cb=>cb.onchange=()=>{cb.checked?sel[tab].add(cb.dataset.pmid):sel[tab].delete(cb.dataset.pmid); summary();});
+    tb.querySelectorAll("button.absbtn").forEach(b=>b.onclick=()=>openModal(rows[+b.dataset.i]));
+  }
+  document.getElementById("pageinfo").textContent=`Page ${page+1}/${TP} · ${rows.length} rows`;
+  document.getElementById("prev").disabled=page===0;
+  document.getElementById("next").disabled=page>=TP-1;
+  summary();
+}
+document.querySelectorAll(".tab").forEach(b=>b.onclick=()=>{tab=b.dataset.tab; page=0; render();});
+document.getElementById("prev").onclick=()=>{if(page>0){page--;render();}};
+document.getElementById("next").onclick=()=>{page++;render();};
+document.getElementById("checkall").onclick=()=>{const rows=curRows(); rows.slice(page*PS,page*PS+PS).forEach(r=>sel[tab].add(r.pmid)); render();};
+document.getElementById("clearall").onclick=()=>{sel[tab].clear(); render();};
+document.getElementById("apply").onclick=()=>{const ids=[...sel[tab]]; if(!ids.length)return; sendPrompt(ACTION[tab](ids));};
+document.getElementById("amodal").addEventListener("click",e=>{if(e.target.id==="amodal")e.target.close();});
+render();
+</script>"""