Wire up collect and parse CLI commands to actual engines

mosaic.py

@@ -224,10 +224,28 @@ def collect(ctx, source, url, name, profile_path, limit, since, date_range, upda
         console.print("[yellow]No source specified.[/yellow] Use --source, --url, or --profile.")
         raise SystemExit(1)
 
-    label = source or url or profile_path
+    from collectors.profile_loader import load_profile, create_adhoc_profile
+    from collectors.custom import CustomSource
+    from utils.cache import DownloadCache
+    from utils.http_limiter import HTTPRateLimiter
+
+    # Load profile
+    try:
+        if profile_path:
+            profile = load_profile(profile_path)
+        elif url:
+            pname = name or url.split('/')[2].replace('.', '_')
+            profile = create_adhoc_profile(url, pname)
+        else:
+            profile = load_profile(source)
+    except (FileNotFoundError, ValueError) as e:
+        console.print(f"[red]Profile error: {e}[/red]")
+        raise SystemExit(1)
+
+    label = profile['name']
     console.print(Panel(
         f"[bold cyan]Collect[/bold cyan]\n\n"
-        f"  Source : {label}\n"
+        f"  Source : {label} — {profile.get('description', '')}\n"
         f"  Limit  : {limit or 'all'}\n"
         f"  Since  : {since or 'n/a'}\n"
         f"  Range  : {' to '.join(date_range) if date_range else 'n/a'}\n"
@@ -235,9 +253,40 @@ def collect(ctx, source, url, name, profile_path, limit, since, date_range, upda
         title="[bold]mosaic collect[/bold]",
         border_style="cyan",
     ))
-    console.print(
-        "\n[dim]Collection not yet implemented — see collectors/[/dim]"
-    )
+
+    db = open_db(ctx.obj["db_path"])
+    try:
+        cache = DownloadCache(os.path.join(ctx.obj["output_dir"], "raw"))
+        cfg = ctx.obj["cfg"]
+        http_cfg = {
+            'timeout': cfg.get('http', 'timeout', fallback='30'),
+            'max_retries': cfg.get('http', 'max_retries', fallback='3'),
+            'user_agent': cfg.get('http', 'user_agent', fallback='Mozilla/5.0 (compatible; research-crawler/1.0)'),
+        }
+        collector = CustomSource(profile, db, cache, config=http_cfg)
+
+        since_date = since
+        until_date = None
+        if date_range:
+            since_date, until_date = date_range
+
+        stats = collector.collect(
+            since=since_date, until=until_date,
+            limit=limit, update=update,
+        )
+
+        table = Table(title="Collection Results", box=box.ROUNDED)
+        table.add_column("Metric", style="bold")
+        table.add_column("Count", justify="right")
+        table.add_row("Discovered", str(stats.get('discovered', 0)))
+        table.add_row("Downloaded", str(stats.get('downloaded', 0)))
+        table.add_row("Already cached", str(stats.get('cached', 0)))
+        table.add_row("Failed", str(stats.get('failed', 0)))
+        if update:
+            table.add_row("Updated", str(stats.get('updated', 0)))
+        console.print(table)
+    finally:
+        db.close()
 
 
 # ---------------------------------------------------------------------------
@@ -253,6 +302,9 @@ def parse(ctx, source, retry_failed):
     source = source or ctx.obj.get("source")
     retry_failed = retry_failed or ctx.obj.get("retry_failed", False)
 
+    from parsers.base import ParserManager
+    from rich.progress import Progress, SpinnerColumn, TextColumn, BarColumn, TaskProgressColumn
+
     console.print(Panel(
         f"[bold green]Parse[/bold green]\n\n"
         f"  Source      : {source or 'all'}\n"
@@ -260,9 +312,80 @@ def parse(ctx, source, retry_failed):
         title="[bold]mosaic parse[/bold]",
         border_style="green",
     ))
-    console.print(
-        "\n[dim]Parsing not yet implemented — see parsers/[/dim]"
-    )
+
+    db = open_db(ctx.obj["db_path"])
+    try:
+        cfg = ctx.obj["cfg"]
+        parser = ParserManager(
+            memory_limit_mb=int(cfg.get('parser', 'subprocess_memory_limit_mb', fallback='512')),
+            timeout_seconds=int(cfg.get('parser', 'subprocess_timeout_seconds', fallback='60')),
+            min_chars_per_page=int(cfg.get('parser', 'min_chars_per_page', fallback='50')),
+            max_pdf_pages=int(cfg.get('parser', 'max_pdf_pages', fallback='200')),
+        )
+
+        # Get documents to parse
+        if source:
+            docs = db.get_documents_by_source(source, status='CACHED')
+        else:
+            docs = db.get_documents_by_source('', status='CACHED')
+            # Get all cached docs across sources
+            cursor = db.conn.execute(
+                "SELECT * FROM documents WHERE status = 'CACHED' AND parse_status IN ('PENDING', ?)",
+                ('PARSE_FAILED' if retry_failed else '__NONE__',)
+            )
+            from storage.models import Document
+            docs = [Document.from_row(row) for row in cursor.fetchall()]
+
+        if not docs:
+            console.print("[yellow]No documents to parse.[/yellow]")
+            return
+
+        parsed = 0
+        failed = 0
+        needs_ocr = 0
+
+        with Progress(
+            SpinnerColumn(), TextColumn("{task.description}"),
+            BarColumn(), TaskProgressColumn(),
+        ) as progress:
+            task = progress.add_task(f"Parsing {len(docs)} docs", total=len(docs))
+            for doc in docs:
+                if doc.parse_status in ('PARSED', 'NEEDS_OCR') and not retry_failed:
+                    progress.advance(task)
+                    continue
+
+                db.update_document_status(doc.id, parse_status='IN_PROGRESS')
+                result = parser.parse(doc.raw_path, doc.doc_type, doc.content_hash)
+
+                if result.success:
+                    doc.text = result.text
+                    doc.title = result.title or doc.title
+                    doc.char_count = result.char_count
+                    if result.metadata:
+                        doc.metadata.update(result.metadata)
+                    ps = 'NEEDS_OCR' if result.needs_ocr else 'PARSED'
+                    doc.parse_status = ps
+                    db.insert_document(doc)
+                    db.update_document_status(doc.id, parse_status=ps)
+                    if result.needs_ocr:
+                        needs_ocr += 1
+                    else:
+                        parsed += 1
+                else:
+                    db.update_document_status(doc.id, parse_status='PARSE_FAILED')
+                    failed += 1
+
+                progress.advance(task)
+
+        table = Table(title="Parse Results", box=box.ROUNDED)
+        table.add_column("Metric", style="bold")
+        table.add_column("Count", justify="right")
+        table.add_row("Parsed", str(parsed))
+        table.add_row("Needs OCR", str(needs_ocr))
+        table.add_row("Failed", str(failed))
+        console.print(table)
+    finally:
+        db.close()
 
 
 # ---------------------------------------------------------------------------