Tests

.gitignore

@@ -1,4 +1,4 @@
-tests/data/*
+#tests/data/*
 
 tests/test_generated/*
 *.DS_STORE

pyproject.toml

@@ -70,4 +70,10 @@ Changelog = "https://github.com/fairscape/fairscape-cli/blob/main/CHANGELOG.md"
 Citation = "https://github.com/fairscape/fairscape-cli/blob/main/CITATION.cff"
 
 [project.scripts]
-fairscape-cli = "fairscape_cli.__main__:cli"
+fairscape-cli = "fairscape_cli.__main__:cli"
+
+[project.optional-dependencies]
+test = [
+    "pytest",
+    "pytest-cov"
+]

src/fairscape_cli/commands/rocrate_commands.py

@@ -881,7 +881,7 @@ def addDataset(
 
         if summary_statistics_source and summary_statistics_destination:
             try:
-                copied_summary_stats_filepath = CopyToROCrate(summary_statistics_source, summary_statistics_destination, rocrate_path)
+                copied_summary_stats_filepath = CopyToROCrate(summary_statistics_source, summary_statistics_destination)
                 click.echo(f"Copied '{summary_statistics_source}' to '{copied_summary_stats_filepath}' inside the crate.")
 
                 summary_stats_guid, summary_stats_instance, computation_instance = generateSummaryStatsElements(

src/fairscape_cli/commands/schema_commands.py

@@ -37,7 +37,7 @@ def schema():
 @click.option('--description', required=True, type=str)
 @click.option('--guid', required=False, type=str, default=None, show_default=False)
 @click.option('--separator', type=str, required=True)
-@click.option('--header', required=False, type=bool, default=False)
+@click.option('--header', required=False, type=bool, default=True)
 @click.argument('schema_file', type=str)
 @click.pass_context
 def create_tabular_schema(

src/fairscape_cli/models/schema/tabular.py

@@ -247,16 +247,15 @@ def validate_file(self, filepath: str) -> List[ValidationError]:
         )
 
         report: Report = resource.validate() 
-
         errors_list = [] 
         if not report.valid:
-            for task_error in report.errors: 
-                for error_detail in task_error.errors: 
+            for task in report.tasks:  # Changed from report.errors
+                for error_detail in task.errors: 
                     validation_error_model = ValidationError( 
                         message=error_detail.message,
                         row=error_detail.row_number if hasattr(error_detail, 'row_number') else None,
                         field=error_detail.field_name if hasattr(error_detail, 'field_name') else None,
-                        failed_keyword=error_detail.code if hasattr(error_detail, 'code') else "error"
+                        failed_keyword=error_detail.type if hasattr(error_detail, 'type') else 'error'
                     )
                     errors_list.append(validation_error_model)
 

tests/commands/augment/test_augment.py

@@ -0,0 +1,294 @@
+import pytest
+import pathlib
+import json
+import shutil
+from fairscape_cli.__main__ import cli as fairscape_cli_app
+
+
+@pytest.fixture
+def mass_spec_crate(tmp_path: pathlib.Path):
+    """
+    Creates a copy of the mass-spec cancer cells RO-Crate for testing augment commands.
+    """
+    source_metadata = pathlib.Path("tests/data/cm4ai-release/mass-spec/cancer-cells/ro-crate-metadata.json")
+
+    crate_dir = tmp_path / "mass-spec-crate"
+    crate_dir.mkdir()
+
+    metadata_file = crate_dir / "ro-crate-metadata.json"
+    shutil.copy2(source_metadata, metadata_file)
+
+    return crate_dir
+
+
+def _load_metadata(crate_path: pathlib.Path):
+    """Helper function to load and return metadata from RO-Crate"""
+    metadata_path = crate_path / "ro-crate-metadata.json"
+    with open(metadata_path, 'r') as f:
+        return json.load(f)
+
+
+class TestAugmentCommands:
+    """Test suite for 'fairscape augment' commands."""
+
+    def test_update_entities_change_root_dataset_name(self, runner, mass_spec_crate: pathlib.Path):
+        """
+        Test updating the root dataset name using MongoDB-style query and update.
+        """
+        query = '{"@type": {"$in": ["Dataset"]}, "@id": "ark:59852/rocrate-data-from-treated-human-cancer-cells/"}'
+        update = '{"$set": {"name": "Updated SEC-MS Dataset - Enhanced Analysis"}}'
+
+        result = runner.invoke(
+            fairscape_cli_app,
+            [
+                "augment", "update-entities", str(mass_spec_crate),
+                "--query", query,
+                "--update", update
+            ]
+        )
+
+        assert result.exit_code == 0, f"CLI Error: {result.output}"
+        assert "Successfully processed entities" in result.output
+
+        metadata = _load_metadata(mass_spec_crate)
+        root_dataset = next(
+            item for item in metadata["@graph"] 
+            if item["@id"] == "ark:59852/rocrate-data-from-treated-human-cancer-cells/"
+        )
+        assert root_dataset["name"] == "Updated SEC-MS Dataset - Enhanced Analysis"
+
+    def test_update_entities_change_version_all_datasets(self, runner, mass_spec_crate: pathlib.Path):
+        """
+        Test updating version for all datasets in the crate.
+        """
+        query = '{"@type": {"$in": ["Dataset"]}, "version": {"$exists": true}}'
+        update = '{"$set": {"version": "2.0"}}'
+
+        result = runner.invoke(
+            fairscape_cli_app,
+            [
+                "augment", "update-entities", str(mass_spec_crate),
+                "--query", query,
+                "--update", update
+            ]
+        )
+
+        assert result.exit_code == 0, f"CLI Error: {result.output}"
+
+        metadata = _load_metadata(mass_spec_crate)
+        datasets_with_version = [
+            item for item in metadata["@graph"]
+            if "Dataset" in (item.get("@type", []) if isinstance(item.get("@type"), list) else [item.get("@type", "")])
+            and "version" in item
+        ]
+
+        for dataset in datasets_with_version:
+            assert dataset["version"] == "2.0"
+
+    def test_update_entities_add_new_field_to_instruments(self, runner, mass_spec_crate: pathlib.Path):
+        """
+        Test adding a new field to all instruments using $set operator.
+        """
+        query = '{"@type": "https://w3id.org/EVI#Instrument"}'
+        update = '{"$set": {"calibrationDate": "2025-01-15", "maintenanceStatus": "verified"}}'
+
+        result = runner.invoke(
+            fairscape_cli_app,
+            [
+                "augment", "update-entities", str(mass_spec_crate),
+                "--query", query,
+                "--update", update
+            ]
+        )
+
+        assert result.exit_code == 0, f"CLI Error: {result.output}"
+
+        metadata = _load_metadata(mass_spec_crate)
+        instruments = [
+            item for item in metadata["@graph"]
+            if item.get("@type") == "https://w3id.org/EVI#Instrument"
+        ]
+
+        for instrument in instruments:
+            assert instrument["calibrationDate"] == "2025-01-15"
+            assert instrument["maintenanceStatus"] == "verified"
+
+    def test_update_entities_modify_experiment_descriptions(self, runner, mass_spec_crate: pathlib.Path):
+        """
+        Test updating experiment descriptions that contain specific text.
+        """
+        query = '{"@type": "https://w3id.org/EVI#Experiment", "name": {"$regex": "Control Experiment"}}'
+        update = '{"$set": {"description": "Updated: SEC-MS profiling of MDA-MB468 breast cancer cell line with enhanced methodology. Each SEC-MS set is composed of 72 fractions with improved precision."}}'
+
+        result = runner.invoke(
+            fairscape_cli_app,
+            [
+                "augment", "update-entities", str(mass_spec_crate),
+                "--query", query,
+                "--update", update
+            ]
+        )
+
+        assert result.exit_code == 0, f"CLI Error: {result.output}"
+
+        metadata = _load_metadata(mass_spec_crate)
+        control_experiments = [
+            item for item in metadata["@graph"]
+            if (item.get("@type") == "https://w3id.org/EVI#Experiment" and 
+                "Control Experiment" in item.get("name", ""))
+        ]
+
+        for experiment in control_experiments:
+            assert "Updated: SEC-MS profiling" in experiment["description"]
+            assert "enhanced methodology" in experiment["description"]
+
+    def test_update_entities_add_keywords_to_samples(self, runner, mass_spec_crate: pathlib.Path):
+        """
+        Test adding keywords to sample entities using $push operator.
+        """
+        query = '{"@type": "https://w3id.org/EVI#Sample"}'
+        update = '{"$push": {"keywords": {"$each": ["validated", "quality-controlled"]}}}'
+
+        result = runner.invoke(
+            fairscape_cli_app,
+            [
+                "augment", "update-entities", str(mass_spec_crate),
+                "--query", query,
+                "--update", update
+            ]
+        )
+
+        assert result.exit_code == 0, f"CLI Error: {result.output}"
+
+        metadata = _load_metadata(mass_spec_crate)
+        samples = [
+            item for item in metadata["@graph"]
+            if item.get("@type") == "https://w3id.org/EVI#Sample"
+        ]
+
+        for sample in samples:
+            assert "validated" in sample["keywords"]
+            assert "quality-controlled" in sample["keywords"]
+
+    def test_update_entities_invalid_query_json(self, runner, mass_spec_crate: pathlib.Path):
+        """
+        Test error handling for invalid JSON in query parameter.
+        """
+        invalid_query = '{"@type": "Dataset", invalid json}'
+        update = '{"$set": {"version": "2.0"}}'
+
+        result = runner.invoke(
+            fairscape_cli_app,
+            [
+                "augment", "update-entities", str(mass_spec_crate),
+                "--query", invalid_query,
+                "--update", update
+            ]
+        )
+
+        assert result.exit_code == 1
+        assert "Invalid JSON in --query string" in result.output
+
+    def test_update_entities_invalid_update_json(self, runner, mass_spec_crate: pathlib.Path):
+        """
+        Test error handling for invalid JSON in update parameter.
+        """
+        query = '{"@type": "Dataset"}'
+        invalid_update = '{"$set": {"version": "2.0", invalid json}}'
+
+        result = runner.invoke(
+            fairscape_cli_app,
+            [
+                "augment", "update-entities", str(mass_spec_crate),
+                "--query", query,
+                "--update", invalid_update
+            ]
+        )
+
+        assert result.exit_code == 1
+        assert "Invalid JSON in --update string" in result.output
+
+    def test_update_entities_no_matches(self, runner, mass_spec_crate: pathlib.Path):
+        """
+        Test behavior when query matches no entities.
+        """
+        query = '{"@type": "NonExistentType"}'
+        update = '{"$set": {"newField": "value"}}'
+
+        result = runner.invoke(
+            fairscape_cli_app,
+            [
+                "augment", "update-entities", str(mass_spec_crate),
+                "--query", query,
+                "--update", update
+            ]
+        )
+
+        assert result.exit_code == 0
+        assert "No entities were modified" in result.output
+
+    def test_update_entities_fails_with_dollar_schema_field(self, runner, mass_spec_crate: pathlib.Path):
+        """
+        Test that adding a $schema field fails due to MongoDB restrictions on $ prefixed fields.
+        """
+        # Query to match the third element in @graph (index 2)
+        query = '{"@id": "ark:59852/cell-line-MDA-MB-468"}'
+        update = '{"$set": {"$schema": "https://example.org/schema.json"}}'
+
+        result = runner.invoke(
+            fairscape_cli_app,
+            [
+                "augment", "update-entities", str(mass_spec_crate),
+                "--query", query,
+                "--update", update
+            ]
+        )
+
+        assert result.exit_code == 1
+
+    def test_link_inverses_success(self, runner, mass_spec_crate: pathlib.Path):
+        """
+        Test successful execution of link-inverses command.
+        """
+        result = runner.invoke(
+            fairscape_cli_app,
+            [
+                "augment", "link-inverses", str(mass_spec_crate)
+            ]
+        )
+
+        assert result.exit_code == 0, f"CLI Error: {result.output}"
+        assert f"Augmenting RO-Crate at: {mass_spec_crate}" in result.output
+        assert "Primary JSON property namespace:" in result.output
+
+    def test_link_inverses_with_custom_namespace(self, runner, mass_spec_crate: pathlib.Path):
+        """
+        Test link-inverses with custom namespace parameter.
+        """
+        custom_namespace = "https://custom.example.org/"
+
+        result = runner.invoke(
+            fairscape_cli_app,
+            [
+                "augment", "link-inverses", str(mass_spec_crate),
+                "--namespace", custom_namespace
+            ]
+        )
+
+        assert result.exit_code == 0, f"CLI Error: {result.output}"
+        assert f"Primary JSON property namespace: {custom_namespace}" in result.output
+
+    def test_link_inverses_nonexistent_rocrate_path(self, runner):
+        """
+        Test link-inverses with nonexistent RO-Crate path.
+        """
+        nonexistent_path = "/tmp/nonexistent/path"
+
+        result = runner.invoke(
+            fairscape_cli_app,
+            [
+                "augment", "link-inverses", nonexistent_path
+            ]
+        )
+
+        assert result.exit_code == 2