Upgrade asta-documents version (#15)

Author: rodneykinney

skills/find-literature/SKILL.md

@@ -29,16 +29,21 @@ Verify installation with `asta literature --help`
 
 Run in background for comprehensive searches (30-60s):
 ```bash
-# Saves to .asta/literature/find/YYYY-MM-DD-HH-MM-SS-{query-slug}.json by default
-Bash(command="asta literature find 'query' --timeout 300", run_in_background=true)
+# Save to a temporary file with explicit -o parameter (required)
+Bash(command="asta literature find 'query' -o /tmp/literature-search-result.json --timeout 300", run_in_background=true)
 ```
-The command saves results to `.asta/literature/find/` (in current working directory) by default with an auto-generated filename.
-The filename is printed to the console when the search is finished. Use the TaskOutput tool to capture the filename for later processing
 
-After the file has been created, index it using the [asta-documents](../asta-documents/SKILL.md) skill.
+After the search completes, move the file to `.asta/documents/literature/find/` and index it:
 
 ```bash
-Bash(command="asta documents add file://<filename> --name=... --summary=...")
+# Create directory if it doesn't exist
+mkdir -p .asta/documents/literature/find
+
+# Move the result file to the documents directory
+mv /tmp/literature-search-result.json .asta/documents/literature/find/
+
+# Index the file using asta-documents
+Bash(command="asta documents add file://.asta/documents/literature/find/literature-search-result.json --name='Literature Search: <query>' --summary='Search results for: <query>'")
 ```
 
 Browse results with jq:

src/asta/literature/find.py

@@ -1,8 +1,6 @@
 """Find papers command"""
 
 import json
-import re
-from datetime import datetime
 from pathlib import Path
 
 import click
@@ -13,6 +11,13 @@
 
 @click.command()
 @click.argument("query")
+@click.option(
+    "-o",
+    "--output",
+    type=click.Path(),
+    required=True,
+    help="Output file path for the results (required)",
+)
 @click.option(
     "--timeout",
     type=int,
@@ -25,24 +30,24 @@
     default="infer",
     help="Search strategy: infer (auto-detect), fast (quick results), or diligent (comprehensive)",
 )
-def find(query: str, timeout: int, mode: str):
+def find(query: str, output: str, timeout: int, mode: str):
     """Find papers matching QUERY using Asta Paper Finder.
 
-    Saves results to .asta/literature/find/ with an auto-generated filename.
+    Requires an output file path to save results.
 
     Examples:
 
-        # Save to default location
-        asta literature find "machine learning in healthcare"
+        # Save to specific file
+        asta literature find "machine learning in healthcare" -o results.json
 
         # With custom timeout
-        asta literature find "transformers" --timeout 60
+        asta literature find "transformers" -o results.json --timeout 60
 
         # Use fast mode for quick results
-        asta literature find "deep learning" --mode fast
+        asta literature find "deep learning" -o results.json --mode fast
 
         # Use diligent mode for comprehensive search
-        asta literature find "neural networks" --mode diligent
+        asta literature find "neural networks" -o results.json --mode diligent
     """
     try:
         client = AstaPaperFinder()
@@ -58,15 +63,9 @@ def find(query: str, timeout: int, mode: str):
         # Convert to dict for output
         output_data = literature_result.model_dump(mode="json", exclude_none=False)
 
-        # Generate default path: .asta/literature/find/YYYY-MM-DD-HH-MM-SS-query-slug.json
-        default_dir = Path.cwd() / ".asta" / "literature" / "find"
-        default_dir.mkdir(parents=True, exist_ok=True)
-
-        timestamp = datetime.now().strftime("%Y-%m-%d-%H-%M-%S")
-        # Create a slug from the query (lowercase, alphanumeric and hyphens only, max 50 chars)
-        query_slug = re.sub(r"[^a-z0-9]+", "-", query.lower()).strip("-")[:50]
-        filename = f"{timestamp}-{query_slug}.json"
-        output_path = default_dir / filename
+        # Use the specified output path
+        output_path = Path(output)
+        output_path.parent.mkdir(parents=True, exist_ok=True)
 
         # Save to file
         with open(output_path, "w") as f:

src/asta/utils/passthrough.conf

@@ -11,9 +11,9 @@
 passthrough {
   documents {
     tool_name = "asta-documents"
-    install_type = "git"
-    install_source = "git+ssh://git@github.com/allenai/asta-resource-repo.git"
-    minimum_version = "0.2.0"
+    install_type = "pypi"
+    install_source = "asta-resource-repository"
+    minimum_version = "0.3.0"
     command_name = "documents"
     friendly_name = "asta-documents"
     docstring = "Manage a local library of documents known to Asta"

tests/test_cli.py

@@ -60,33 +60,30 @@ def test_find_success_file_output(self, runner, tmp_path):
         }
 
         with patch("asta.literature.find.AstaPaperFinder") as MockFinder:
-            with patch("asta.literature.find.Path.cwd", return_value=tmp_path):
-                mock_instance = MagicMock()
-                mock_instance.find_papers.return_value = mock_result
-                MockFinder.return_value = mock_instance
+            mock_instance = MagicMock()
+            mock_instance.find_papers.return_value = mock_result
+            MockFinder.return_value = mock_instance
 
-                result = runner.invoke(cli, ["literature", "find", "test query"])
+            output_file = tmp_path / "results.json"
+            result = runner.invoke(
+                cli, ["literature", "find", "test query", "-o", str(output_file)]
+            )
 
         assert result.exit_code == 0
 
-        # Verify file was created in default location
-        output_dir = tmp_path / ".asta" / "literature" / "find"
-        assert output_dir.exists()
-
-        # Find the created file (should match pattern: YYYY-MM-DD-HH-MM-SS-test-query.json)
-        json_files = list(output_dir.glob("*-test-query.json"))
-        assert len(json_files) == 1
+        # Verify file was created at specified location
+        assert output_file.exists()
 
         # Verify file contents
-        with open(json_files[0]) as f:
+        with open(output_file) as f:
             data = json.load(f)
 
         assert data["query"] == "test query"
         assert len(data["results"]) == 2
         assert data["results"][0]["corpusId"] == 123
         assert data["results"][1]["corpusId"] == 456
 
-    def test_find_timeout_error(self, runner):
+    def test_find_timeout_error(self, runner, tmp_path):
         """Test find command with timeout error."""
         with patch("asta.literature.find.AstaPaperFinder") as MockFinder:
             mock_instance = MagicMock()
@@ -95,22 +92,28 @@ def test_find_timeout_error(self, runner):
             )
             MockFinder.return_value = mock_instance
 
-            result = runner.invoke(cli, ["literature", "find", "test query"])
+            output_file = tmp_path / "results.json"
+            result = runner.invoke(
+                cli, ["literature", "find", "test query", "-o", str(output_file)]
+            )
 
         assert result.exit_code == 2
 
-    def test_find_general_error(self, runner):
+    def test_find_general_error(self, runner, tmp_path):
         """Test find command with general error."""
         with patch("asta.literature.find.AstaPaperFinder") as MockFinder:
             mock_instance = MagicMock()
             mock_instance.find_papers.side_effect = Exception("API error")
             MockFinder.return_value = mock_instance
 
-            result = runner.invoke(cli, ["literature", "find", "test query"])
+            output_file = tmp_path / "results.json"
+            result = runner.invoke(
+                cli, ["literature", "find", "test query", "-o", str(output_file)]
+            )
 
         assert result.exit_code == 1
 
-    def test_find_custom_timeout(self, runner):
+    def test_find_custom_timeout(self, runner, tmp_path):
         """Test find command with custom timeout."""
         mock_result = {
             "query": "test query",
@@ -134,16 +137,26 @@ def test_find_custom_timeout(self, runner):
             mock_instance.find_papers.return_value = mock_result
             MockFinder.return_value = mock_instance
 
+            output_file = tmp_path / "results.json"
             result = runner.invoke(
-                cli, ["literature", "find", "test query", "--timeout", "60"]
+                cli,
+                [
+                    "literature",
+                    "find",
+                    "test query",
+                    "-o",
+                    str(output_file),
+                    "--timeout",
+                    "60",
+                ],
             )
 
         assert result.exit_code == 0
         mock_instance.find_papers.assert_called_once_with(
             "test query", timeout=60, save_to_file=None, operation_mode="infer"
         )
 
-    def test_find_with_mode_option(self, runner):
+    def test_find_with_mode_option(self, runner, tmp_path):
         """Test find command with different operation modes."""
         mock_result = {
             "query": "test query",
@@ -166,9 +179,19 @@ def test_find_with_mode_option(self, runner):
             mock_instance.find_papers.return_value = mock_result
             MockFinder.return_value = mock_instance
 
+            output_file = tmp_path / "results.json"
             # Test fast mode
             result = runner.invoke(
-                cli, ["literature", "find", "test query", "--mode", "fast"]
+                cli,
+                [
+                    "literature",
+                    "find",
+                    "test query",
+                    "-o",
+                    str(output_file),
+                    "--mode",
+                    "fast",
+                ],
             )
 
         assert result.exit_code == 0
@@ -413,11 +436,10 @@ def test_documents_config(self):
 
         # Should have required fields
         assert config["tool_name"] == "asta-documents"
-        assert "install_type" in config
-        assert config["install_type"] in ("pypi", "git", "local")
-        assert "minimum_version" in config
+        assert config["install_type"] == "pypi"
+        assert config["install_source"] == "asta-resource-repository"
+        assert config["minimum_version"] == "0.3.0"
         assert validate_semver(config["minimum_version"])
-        assert "install_source" in config
         assert config["command_name"] == "documents"
 
     def test_documents_help_requires_installation(self, runner):