merge-duplicates slice and did a first polish

src/repo_registry/core/service.py

@@ -394,6 +394,102 @@ class RegistryService:
         self.store.update_repository_status(repository_id, "reviewing")
         return self.store.get_candidate_graph(repository_id, analysis_run_id)
 
+    def merge_candidate_ability(
+        self,
+        repository_id: int,
+        analysis_run_id: int,
+        source_ability_id: int,
+        *,
+        target_ability_id: int,
+        notes: str = "",
+    ) -> CandidateGraph:
+        self.store.merge_candidate_ability(
+            repository_id,
+            analysis_run_id,
+            source_ability_id,
+            target_ability_id,
+        )
+        self.store.create_review_decision(
+            repository_id,
+            analysis_run_id,
+            action="merge_candidate_ability",
+            notes=notes,
+        )
+        self.store.update_repository_status(repository_id, "reviewing")
+        return self.store.get_candidate_graph(repository_id, analysis_run_id)
+
+    def merge_candidate_capability(
+        self,
+        repository_id: int,
+        analysis_run_id: int,
+        source_capability_id: int,
+        *,
+        target_capability_id: int,
+        notes: str = "",
+    ) -> CandidateGraph:
+        self.store.merge_candidate_capability(
+            repository_id,
+            analysis_run_id,
+            source_capability_id,
+            target_capability_id,
+        )
+        self.store.create_review_decision(
+            repository_id,
+            analysis_run_id,
+            action="merge_candidate_capability",
+            notes=notes,
+        )
+        self.store.update_repository_status(repository_id, "reviewing")
+        return self.store.get_candidate_graph(repository_id, analysis_run_id)
+
+    def merge_candidate_feature(
+        self,
+        repository_id: int,
+        analysis_run_id: int,
+        source_feature_id: int,
+        *,
+        target_feature_id: int,
+        notes: str = "",
+    ) -> CandidateGraph:
+        self.store.merge_candidate_feature(
+            repository_id,
+            analysis_run_id,
+            source_feature_id,
+            target_feature_id,
+        )
+        self.store.create_review_decision(
+            repository_id,
+            analysis_run_id,
+            action="merge_candidate_feature",
+            notes=notes,
+        )
+        self.store.update_repository_status(repository_id, "reviewing")
+        return self.store.get_candidate_graph(repository_id, analysis_run_id)
+
+    def merge_candidate_evidence(
+        self,
+        repository_id: int,
+        analysis_run_id: int,
+        source_evidence_id: int,
+        *,
+        target_evidence_id: int,
+        notes: str = "",
+    ) -> CandidateGraph:
+        self.store.merge_candidate_evidence(
+            repository_id,
+            analysis_run_id,
+            source_evidence_id,
+            target_evidence_id,
+        )
+        self.store.create_review_decision(
+            repository_id,
+            analysis_run_id,
+            action="merge_candidate_evidence",
+            notes=notes,
+        )
+        self.store.update_repository_status(repository_id, "reviewing")
+        return self.store.get_candidate_graph(repository_id, analysis_run_id)
+
     def add_ability(
         self,
         repository_id: int,

src/repo_registry/storage/sqlite.py

@@ -643,6 +643,132 @@ class RegistryStore:
             target_capability_id=target_capability_id,
         )
 
+    def merge_candidate_ability(
+        self,
+        repository_id: int,
+        analysis_run_id: int,
+        source_ability_id: int,
+        target_ability_id: int,
+    ) -> None:
+        if source_ability_id == target_ability_id:
+            raise ValueError("source and target candidate ability must be different")
+        self._ensure_candidate_row(
+            table="candidate_abilities",
+            label="target candidate ability",
+            repository_id=repository_id,
+            analysis_run_id=analysis_run_id,
+            candidate_id=target_ability_id,
+        )
+        with self.connect() as connection:
+            cursor = connection.execute(
+                """
+                UPDATE candidate_abilities
+                SET status = 'merged'
+                WHERE id = ?
+                  AND repository_id = ?
+                  AND analysis_run_id = ?
+                  AND status = 'candidate'
+                """,
+                (source_ability_id, repository_id, analysis_run_id),
+            )
+            if cursor.rowcount == 0:
+                raise NotFoundError(
+                    "source candidate ability "
+                    f"{source_ability_id} was not found for repository "
+                    f"{repository_id} analysis run {analysis_run_id}"
+                )
+            connection.execute(
+                """
+                UPDATE candidate_capabilities
+                SET ability_id = ?
+                WHERE ability_id = ? AND repository_id = ? AND analysis_run_id = ?
+                """,
+                (target_ability_id, source_ability_id, repository_id, analysis_run_id),
+            )
+
+    def merge_candidate_capability(
+        self,
+        repository_id: int,
+        analysis_run_id: int,
+        source_capability_id: int,
+        target_capability_id: int,
+    ) -> None:
+        if source_capability_id == target_capability_id:
+            raise ValueError("source and target candidate capability must be different")
+        self._ensure_candidate_row(
+            table="candidate_capabilities",
+            label="target candidate capability",
+            repository_id=repository_id,
+            analysis_run_id=analysis_run_id,
+            candidate_id=target_capability_id,
+        )
+        with self.connect() as connection:
+            cursor = connection.execute(
+                """
+                UPDATE candidate_capabilities
+                SET status = 'merged'
+                WHERE id = ?
+                  AND repository_id = ?
+                  AND analysis_run_id = ?
+                  AND status = 'candidate'
+                """,
+                (source_capability_id, repository_id, analysis_run_id),
+            )
+            if cursor.rowcount == 0:
+                raise NotFoundError(
+                    "source candidate capability "
+                    f"{source_capability_id} was not found for repository "
+                    f"{repository_id} analysis run {analysis_run_id}"
+                )
+            for table in ("candidate_features", "candidate_evidence"):
+                connection.execute(
+                    f"""
+                    UPDATE {table}
+                    SET capability_id = ?
+                    WHERE capability_id = ?
+                      AND repository_id = ?
+                      AND analysis_run_id = ?
+                    """,
+                    (
+                        target_capability_id,
+                        source_capability_id,
+                        repository_id,
+                        analysis_run_id,
+                    ),
+                )
+
+    def merge_candidate_feature(
+        self,
+        repository_id: int,
+        analysis_run_id: int,
+        source_feature_id: int,
+        target_feature_id: int,
+    ) -> None:
+        self._merge_candidate_leaf(
+            table="candidate_features",
+            label="candidate feature",
+            repository_id=repository_id,
+            analysis_run_id=analysis_run_id,
+            source_id=source_feature_id,
+            target_id=target_feature_id,
+        )
+
+    def merge_candidate_evidence(
+        self,
+        repository_id: int,
+        analysis_run_id: int,
+        source_evidence_id: int,
+        target_evidence_id: int,
+    ) -> None:
+        self._merge_candidate_leaf(
+            table="candidate_evidence",
+            label="candidate evidence",
+            repository_id=repository_id,
+            analysis_run_id=analysis_run_id,
+            source_id=source_evidence_id,
+            target_id=target_evidence_id,
+        )
+
     def _ensure_candidate_row(
         self,
         *,
@@ -703,6 +829,43 @@ class RegistryStore:
                 f"{repository_id} analysis run {analysis_run_id}"
             )
 
+    def _merge_candidate_leaf(
+        self,
+        *,
+        table: str,
+        label: str,
+        repository_id: int,
+        analysis_run_id: int,
+        source_id: int,
+        target_id: int,
+    ) -> None:
+        if source_id == target_id:
+            raise ValueError(f"source and target {label} must be different")
+        self._ensure_candidate_row(
+            table=table,
+            label=f"target {label}",
+            repository_id=repository_id,
+            analysis_run_id=analysis_run_id,
+            candidate_id=target_id,
+        )
+        with self.connect() as connection:
+            cursor = connection.execute(
+                f"""
+                UPDATE {table}
+                SET status = 'merged'
+                WHERE id = ?
+                  AND repository_id = ?
+                  AND analysis_run_id = ?
+                  AND status = 'candidate'
+                """,
+                (source_id, repository_id, analysis_run_id),
+            )
+        if cursor.rowcount == 0:
+            raise NotFoundError(
+                f"source {label} {source_id} was not found for repository "
+                f"{repository_id} analysis run {analysis_run_id}"
+            )
+
     def _reject_candidate_leaf(
         self,
         *,

src/repo_registry/web_api/app.py

@@ -94,6 +94,26 @@ class CandidateLeafRelink(BaseModel):
     notes: str = ""
 
 
+class CandidateAbilityMerge(BaseModel):
+    target_ability_id: int
+    notes: str = ""
+
+
+class CandidateCapabilityMerge(BaseModel):
+    target_capability_id: int
+    notes: str = ""
+
+
+class CandidateFeatureMerge(BaseModel):
+    target_feature_id: int
+    notes: str = ""
+
+
+class CandidateEvidenceMerge(BaseModel):
+    target_evidence_id: int
+    notes: str = ""
+
+
 app = FastAPI(title="Repository Ability Registry", version="0.1.0")
 
 
@@ -426,6 +446,102 @@ def relink_candidate_evidence(
         raise HTTPException(status_code=404, detail=str(exc)) from exc
 
 
+@app.post(
+    "/repos/{repository_id}/analysis-runs/{analysis_run_id}"
+    "/candidate-abilities/{source_ability_id}/merge"
+)
+def merge_candidate_ability(
+    repository_id: int,
+    analysis_run_id: int,
+    source_ability_id: int,
+    payload: CandidateAbilityMerge,
+    service: RegistryService = Depends(get_service),
+) -> dict[str, object]:
+    try:
+        return asdict(
+            service.merge_candidate_ability(
+                repository_id,
+                analysis_run_id,
+                source_ability_id,
+                **payload.model_dump(),
+            )
+        )
+    except (NotFoundError, ValueError) as exc:
+        raise HTTPException(status_code=400, detail=str(exc)) from exc
+
+
+@app.post(
+    "/repos/{repository_id}/analysis-runs/{analysis_run_id}"
+    "/candidate-capabilities/{source_capability_id}/merge"
+)
+def merge_candidate_capability(
+    repository_id: int,
+    analysis_run_id: int,
+    source_capability_id: int,
+    payload: CandidateCapabilityMerge,
+    service: RegistryService = Depends(get_service),
+) -> dict[str, object]:
+    try:
+        return asdict(
+            service.merge_candidate_capability(
+                repository_id,
+                analysis_run_id,
+                source_capability_id,
+                **payload.model_dump(),
+            )
+        )
+    except (NotFoundError, ValueError) as exc:
+        raise HTTPException(status_code=400, detail=str(exc)) from exc
+
+
+@app.post(
+    "/repos/{repository_id}/analysis-runs/{analysis_run_id}"
+    "/candidate-features/{source_feature_id}/merge"
+)
+def merge_candidate_feature(
+    repository_id: int,
+    analysis_run_id: int,
+    source_feature_id: int,
+    payload: CandidateFeatureMerge,
+    service: RegistryService = Depends(get_service),
+) -> dict[str, object]:
+    try:
+        return asdict(
+            service.merge_candidate_feature(
+                repository_id,
+                analysis_run_id,
+                source_feature_id,
+                **payload.model_dump(),
+            )
+        )
+    except (NotFoundError, ValueError) as exc:
+        raise HTTPException(status_code=400, detail=str(exc)) from exc
+
+
+@app.post(
+    "/repos/{repository_id}/analysis-runs/{analysis_run_id}"
+    "/candidate-evidence/{source_evidence_id}/merge"
+)
+def merge_candidate_evidence(
+    repository_id: int,
+    analysis_run_id: int,
+    source_evidence_id: int,
+    payload: CandidateEvidenceMerge,
+    service: RegistryService = Depends(get_service),
+) -> dict[str, object]:
+    try:
+        return asdict(
+            service.merge_candidate_evidence(
+                repository_id,
+                analysis_run_id,
+                source_evidence_id,
+                **payload.model_dump(),
+            )
+        )
+    except (NotFoundError, ValueError) as exc:
+        raise HTTPException(status_code=400, detail=str(exc)) from exc
+
+
 @app.post("/repos/{repository_id}/abilities", status_code=201)
 def create_ability(
     repository_id: int,

src/repo_registry/web_ui/views.py

@@ -124,7 +124,10 @@ def page(title: str, body: str) -> HTMLResponse:
           <body>
             <header>
               <a href="/ui"><strong>Repository Ability Registry</strong></a>
-              <a href="/docs">API Docs</a>
+              <nav class="actions">
+                <a href="/ui/search">Search</a>
+                <a href="/docs">API Docs</a>
+              </nav>
             </header>
             <main>{body}</main>
           </body>
@@ -170,6 +173,49 @@ def repository_index(service: RegistryService = Depends(get_service)) -> HTMLRes
     return page("Repositories", body)
 
 
+@router.get("/ui/search")
+def search_page(
+    q: str = "",
+    service: RegistryService = Depends(get_service),
+) -> HTMLResponse:
+    results = service.search(q) if q.strip() else []
+    rows = "\n".join(
+        f"""
+        <tr>
+          <td><a href="/ui/repos/{result.repository_id}">{escape(result.repository_name)}</a></td>
+          <td><span class="pill">{escape(result.match_type)}</span></td>
+          <td>{escape(result.match_name)}</td>
+          <td>{result.confidence:.2f}</td>
+        </tr>
+        """
+        for result in results
+    )
+    empty = (
+        '<tr><td colspan="4" class="muted">No matches.</td></tr>'
+        if q.strip()
+        else '<tr><td colspan="4" class="muted">Enter a need, capability, or repository name.</td></tr>'
+    )
+    body = f"""
+    <div class="actions">
+      <h1 style="margin-right:auto">Search</h1>
+      <a class="button secondary" href="/ui">Repositories</a>
+    </div>
+    <section class="panel">
+      <form class="actions" method="get" action="/ui/search">
+        <input name="q" value="{escape(q)}" placeholder="Search approved registry entries">
+        <button type="submit">Search</button>
+      </form>
+    </section>
+    <section class="panel" style="margin-top:18px">
+      <table>
+        <thead><tr><th>Repository</th><th>Match</th><th>Name</th><th>Confidence</th></tr></thead>
+        <tbody>{rows or empty}</tbody>
+      </table>
+    </section>
+    """
+    return page("Search", body)
+
+
 @router.post("/ui/repos")
 def create_repository_from_form(
     url: str = Form(...),
@@ -524,6 +570,102 @@ def relink_candidate_evidence_from_form(
     )
 
 
+@router.post(
+    "/ui/repos/{repository_id}/analysis-runs/{analysis_run_id}"
+    "/candidate-abilities/{source_ability_id}/merge"
+)
+def merge_candidate_ability_from_form(
+    repository_id: int,
+    analysis_run_id: int,
+    source_ability_id: int,
+    target_ability_id: int = Form(...),
+    service: RegistryService = Depends(get_service),
+) -> RedirectResponse:
+    service.merge_candidate_ability(
+        repository_id,
+        analysis_run_id,
+        source_ability_id,
+        target_ability_id=target_ability_id,
+        notes="Merged from web UI",
+    )
+    return RedirectResponse(
+        f"/ui/repos/{repository_id}/analysis-runs/{analysis_run_id}",
+        status_code=303,
+    )
+
+
+@router.post(
+    "/ui/repos/{repository_id}/analysis-runs/{analysis_run_id}"
+    "/candidate-capabilities/{source_capability_id}/merge"
+)
+def merge_candidate_capability_from_form(
+    repository_id: int,
+    analysis_run_id: int,
+    source_capability_id: int,
+    target_capability_id: int = Form(...),
+    service: RegistryService = Depends(get_service),
+) -> RedirectResponse:
+    service.merge_candidate_capability(
+        repository_id,
+        analysis_run_id,
+        source_capability_id,
+        target_capability_id=target_capability_id,
+        notes="Merged from web UI",
+    )
+    return RedirectResponse(
+        f"/ui/repos/{repository_id}/analysis-runs/{analysis_run_id}",
+        status_code=303,
+    )
+
+
+@router.post(
+    "/ui/repos/{repository_id}/analysis-runs/{analysis_run_id}"
+    "/candidate-features/{source_feature_id}/merge"
+)
+def merge_candidate_feature_from_form(
+    repository_id: int,
+    analysis_run_id: int,
+    source_feature_id: int,
+    target_feature_id: int = Form(...),
+    service: RegistryService = Depends(get_service),
+) -> RedirectResponse:
+    service.merge_candidate_feature(
+        repository_id,
+        analysis_run_id,
+        source_feature_id,
+        target_feature_id=target_feature_id,
+        notes="Merged from web UI",
+    )
+    return RedirectResponse(
+        f"/ui/repos/{repository_id}/analysis-runs/{analysis_run_id}",
+        status_code=303,
+    )
+
+
+@router.post(
+    "/ui/repos/{repository_id}/analysis-runs/{analysis_run_id}"
+    "/candidate-evidence/{source_evidence_id}/merge"
+)
+def merge_candidate_evidence_from_form(
+    repository_id: int,
+    analysis_run_id: int,
+    source_evidence_id: int,
+    target_evidence_id: int = Form(...),
+    service: RegistryService = Depends(get_service),
+) -> RedirectResponse:
+    service.merge_candidate_evidence(
+        repository_id,
+        analysis_run_id,
+        source_evidence_id,
+        target_evidence_id=target_evidence_id,
+        notes="Merged from web UI",
+    )
+    return RedirectResponse(
+        f"/ui/repos/{repository_id}/analysis-runs/{analysis_run_id}",
+        status_code=303,
+    )
+
+
 def render_candidate_graph(graph: dict, repository_id: int, analysis_run_id: int) -> str:
     abilities = graph.get("abilities", [])
     if not abilities:
@@ -538,11 +680,13 @@ def render_candidate_graph(graph: dict, repository_id: int, analysis_run_id: int
             f"""
             <li>
               <strong>{escape(ability['name'])}</strong>
+              <span class="pill">ID {ability['id']}</span>
               <span class="pill">{escape(ability['status'])}</span>
               <span class="pill">{ability['confidence']:.2f}</span>
               {render_candidate_ability_actions(ability, repository_id, analysis_run_id)}
               <p class="muted">{escape(ability['description'])}</p>
               {render_candidate_edit_form('candidate-abilities', ability, repository_id, analysis_run_id)}
+              {render_candidate_merge_form('candidate-abilities', ability, repository_id, analysis_run_id, 'target_ability_id', 'Merge into ability ID')}
               {render_sources(ability['source_refs'])}
               <ul>{capabilities}</ul>
             </li>
@@ -608,12 +752,14 @@ def render_candidate_capability(
     return f"""
     <li>
       <strong>{escape(capability['name'])}</strong>
+      <span class="pill">ID {capability['id']}</span>
       <span class="pill">{escape(capability['status'])}</span>
       <span class="pill">{capability['confidence']:.2f}</span>
       {render_candidate_reject_form('candidate-capabilities', capability, repository_id, analysis_run_id)}
       <p class="muted">{escape(capability['description'])}</p>
       {render_candidate_edit_form('candidate-capabilities', capability, repository_id, analysis_run_id)}
       {render_candidate_relink_form('candidate-capabilities', capability, repository_id, analysis_run_id, 'target_ability_id', 'Target ability ID')}
+      {render_candidate_merge_form('candidate-capabilities', capability, repository_id, analysis_run_id, 'target_capability_id', 'Merge into capability ID')}
       {render_sources(capability['source_refs'])}
       <h3>Features</h3>
       <ul>{features or '<li class="muted">No feature candidates.</li>'}</ul>
@@ -631,11 +777,13 @@ def render_candidate_feature(
     return f"""
     <li>
       {escape(feature["name"])}
+      <span class="pill">ID {feature["id"]}</span>
       <span class="pill">{escape(feature["status"])}</span>
       <span class="pill">{escape(feature["type"])}</span>
       <span class="source">{escape(feature["location"])}</span>
       {render_candidate_reject_form('candidate-features', feature, repository_id, analysis_run_id)}
       {render_candidate_relink_form('candidate-features', feature, repository_id, analysis_run_id, 'target_capability_id', 'Target capability ID')}
+      {render_candidate_merge_form('candidate-features', feature, repository_id, analysis_run_id, 'target_feature_id', 'Merge into feature ID')}
     </li>
     """
 
@@ -648,11 +796,13 @@ def render_candidate_evidence(
     return f"""
     <li>
       {escape(evidence["type"])}
+      <span class="pill">ID {evidence["id"]}</span>
       <span class="pill">{escape(evidence["status"])}</span>
       <span class="pill">{escape(evidence["strength"])}</span>
       <span class="source">{escape(evidence["reference"])}</span>
       {render_candidate_reject_form('candidate-evidence', evidence, repository_id, analysis_run_id)}
       {render_candidate_relink_form('candidate-evidence', evidence, repository_id, analysis_run_id, 'target_capability_id', 'Target capability ID')}
+      {render_candidate_merge_form('candidate-evidence', evidence, repository_id, analysis_run_id, 'target_evidence_id', 'Merge into evidence ID')}
     </li>
     """
 
@@ -698,6 +848,28 @@ def render_candidate_relink_form(
     """
 
 
+def render_candidate_merge_form(
+    collection: str,
+    candidate: dict,
+    repository_id: int,
+    analysis_run_id: int,
+    field_name: str,
+    label: str,
+) -> str:
+    if candidate["status"] != "candidate":
+        return ""
+    action = (
+        f"/ui/repos/{repository_id}/analysis-runs/{analysis_run_id}"
+        f"/{collection}/{candidate['id']}/merge"
+    )
+    return f"""
+    <form style="display:inline-grid; grid-template-columns: 140px auto; gap: 6px; align-items: end;" method="post" action="{action}">
+      <label>{label}<input name="{field_name}" type="number" min="1" required></label>
+      <button class="secondary" type="submit">Merge</button>
+    </form>
+    """
+
+
 def render_ability_map(ability_map: dict) -> str:
     abilities = ability_map.get("abilities", [])
     if not abilities: