feat!: generalize script by removing organizational metadata

Remove Phase class, organizational metadata blocks, and unused project fields. Update configuration
to use 'default_grants' and simplify PI usage to fallback corresponding author determination only.

BREAKING CHANGES: - Remove 'phase' and 'project' fields from configuration - Use 'default_grants'
instead of 'default_grant' - Generate only standard Dataverse citation metadata

.gitignore

@@ -1,5 +1,6 @@
 # Config file
 config.yaml
+.config.yaml
 
 # Processed DOIs
 *.json

README.md

@@ -8,7 +8,14 @@
 
 - **DOI Validation and Normalization:** Validates DOIs and converts them into a standardized format.
 - **Metadata Retrieval:** Fetches metadata such as title, abstract, license, and author information from external sources.
-- **Metadata Mapping:** Automatically maps and generates metadata fields (e.g., title, description, keywords) including support for controlled vocabularies and compound fields.
+- **Standard Dataverse Metadata:** Generates standard Dataverse citation metadata including:
+  - Title, publication date, and alternative URL
+  - Author information with affiliations and ORCID identifiers
+  - Dataset contact information (corresponding authors)
+  - Abstract and description
+  - Keywords and subject classification
+  - Grant/funding information
+  - License information when available
 - **Optional Upload:** Allows uploading of metadata directly to a Dataverse.org server.
 - **Progress Tracking:** Uses the Rich library for user-friendly progress tracking and error handling.
 
@@ -23,14 +30,41 @@ cd doi2dataset
 
 ## Configuration
 
-Configuration
-
 Before running the tool, configure the necessary settings in the `config.yaml` file located in the project root. This file contains configuration details such as:
 
-- Connection details (URL, API token, authentication credentials)
+- **Connection details**: URL, API token, authentication credentials for Dataverse server
-- Mapping of project phases
+- **Principal Investigator (PI) information**: Optional - used for fallback determination of corresponding authors when not explicitly specified in the publication
-- Principal Investigator (PI) information
+- **Default grant configurations**: Funding information to be included in the metadata (supports multiple grants)
-- Default grant configurations
+
+### Configuration File Structure
+
+The configuration file should follow this structure:
+
+```yaml
+# Dataverse server connection details
+dataverse:
+  url: "https://your-dataverse-instance.org"
+  api_token: "your-api-token"
+
+# Default grant information (supports multiple grants)
+default_grants:
+  - funder: "Your Funding Agency"
+    id: "GRANT123456"
+  - funder: "Another Funding Agency"
+    id: "GRANT789012"
+
+# Principal investigators for fallback corresponding author determination (optional)
+pis:
+  - family_name: "Doe"
+    given_name: "John"
+    orcid: "0000-0000-0000-0000"
+    email: "john.doe@university.edu"
+    affiliation: "Department of Science, University"
+```
+
+See `config_example.yaml` for a complete example configuration.
+
+**Note**: The PI section is optional. If no corresponding authors are found in the publication metadata and no PIs are configured, the tool will still generate metadata but may issue a warning about missing corresponding author information.
 
 ## Usage
 
@@ -102,11 +136,13 @@ pytest --cov=. --cov-report=html
 This creates a `htmlcov` directory. Open `htmlcov/index.html` in a browser to view the detailed coverage report.
 
 A `.coveragerc` configuration file is provided that:
+
 - Excludes test files, documentation, and boilerplate code from coverage analysis
 - Configures reporting to ignore common non-testable lines (like defensive imports)
 - Sets the output directory for HTML reports
 
 Recent improvements have increased coverage from 48% to 61% by adding focused tests for:
+
 - Citation building functionality
 - License processing and validation
 - Metadata field extraction
@@ -114,6 +150,7 @@ Recent improvements have increased coverage from 48% to 61% by adding focused te
 - Publication data parsing and validation
 
 Areas that could benefit from additional testing:
+
 - More edge cases in the MetadataProcessor class workflow
 - Additional CitationBuilder scenarios with diverse inputs
 - Complex network interactions and error handling
@@ -122,7 +159,7 @@ Areas that could benefit from additional testing:
 
 The test suite is organized into six main files:
 
-1. **test_doi2dataset.py**: Basic tests for core functions like phase checking, name splitting and DOI validation.
+1. **test_doi2dataset.py**: Basic tests for core functions like name splitting, DOI validation, and filename sanitization.
 2. **test_fetch_doi_mock.py**: Tests API interactions using a mock OpenAlex response stored in `srep45389.json`.
 3. **test_citation_builder.py**: Tests for building citation metadata from API responses.
 4. **test_metadata_processor.py**: Tests for the metadata processing workflow.
@@ -136,7 +173,6 @@ The test suite covers the following categories of functionality:
 #### Core Functionality Tests
 
 - **DOI Validation and Processing**: Parameterized tests for DOI normalization, validation, and filename sanitization with various inputs.
-- **Phase Management**: Tests for checking publication year against defined project phases, including boundary cases.
 - **Name Processing**: Extensive tests for parsing and splitting author names in different formats (with/without commas, middle initials, etc.).
 - **Email Validation**: Tests for proper validation of email addresses with various domain configurations.
 
@@ -151,12 +187,36 @@ The test suite covers the following categories of functionality:
 
 - **Citation Building**: Tests for properly building citation metadata from API responses.
 - **License Processing**: Tests for correctly identifying and formatting license information from various license IDs.
-- **Principal Investigator Matching**: Tests for finding project PIs based on ORCID identifiers.
+- **Principal Investigator Matching**: Tests for finding project PIs based on ORCID identifiers (used for fallback corresponding author determination).
 - **Configuration Loading**: Tests for properly loading and validating configuration from files.
 - **Metadata Workflow**: Tests for the complete metadata processing workflow.
 
 These tests ensure that all components work correctly in isolation and together as a system, with special attention to edge cases and error handling.
 
+## Changelog
+
+### Version 0.2.0 - Generalization Update
+
+This version has been updated to make the tool more generalized and suitable for broader use cases:
+
+**Breaking Changes:**
+
+- Removed organizational-specific metadata blocks (project phases, organizational fields)
+- Removed `Phase` class and phase-related configuration
+- Simplified configuration structure
+
+**What's New:**
+
+- Streamlined metadata generation focusing on standard Dataverse citation metadata
+- Reduced configuration requirements for easier adoption
+- Maintained PI information support for corresponding author fallback functionality
+
+**Migration Guide:**
+
+- Remove the `phase` section from your configuration file
+- The tool will now generate only standard citation metadata blocks
+- PI information is still supported and used for fallback corresponding author determination
+
 ## Contributing
 
 Contributions are welcome! Please fork the repository and submit a pull request with your improvements.

__init__.py

@@ -8,9 +8,8 @@ from .doi2dataset import (
     LicenseProcessor,
     MetadataProcessor,
     NameProcessor,
-    PIFinder,
     Person,
-    Phase,
+    PIFinder,
     SubjectMapper,
     sanitize_filename,
     validate_email_address,

config_example.yaml

@@ -1,23 +1,25 @@
-default_grant:
+dataverse:
+  url: "https://your-dataverse-instance.org"
+  api_token: "your-api-token-here"
+  dataverse: "your-dataverse-alias"
+  auth_user: "your-username"
+  auth_password: "your-password"
+
+default_grants:
   - funder: "Awesome Funding Agency"
     id: "ABC12345"
-
+  - funder: "Another Funding Agency"
-phase:
+    id: "DEF67890"
-  "Phase 1 (2021/2025)":
-    start: 2021
-    end: 2025
 
 pis:
   - family_name: "Doe"
     given_name: "Jon"
     orcid: "0000-0000-0000-0000"
-    email: "jon.doe@some-university.edu"
+    email: "jon.doe@iana.org"
     affiliation: "Institute of Science, Some University"
-    project: ["Project A01"]
 
   - family_name: "Doe"
     given_name: "Jane"
     orcid: "0000-0000-0000-0001"
-    email: "jane.doe@some-university.edu"
+    email: "jane.doe@iana.org"
     affiliation: "Institute of Science, Some University"
-    project: ["Project A02"]

doi2dataset.py

@@ -109,36 +109,6 @@ class FieldType(Enum):
     COMPOUND = "compound"
     VOCABULARY = "controlledVocabulary"
 
-@dataclass
-class Phase:
-    """
-    Represents a project phase with a defined time span.
-
-    Attributes:
-        name (str): The name of the project phase.
-        start (int): The start year of the project phase.
-        end (int): The end year of the project phase.
-    """
-
-    name: str
-    start: int
-    end: int
-
-    def check_year(self, year: int) -> bool:
-        """
-        Checks whether a given year falls within the project's phase boundaries.
-
-        Args:
-            year (int): The year to check.
-
-        Returns:
-            bool: True if the year is within the phase boundaries, otherwise False.
-        """
-
-        if self.start <= year <= self.end:
-            return True
-        return False
-
 @dataclass
 class BaseMetadataField[T]:
     """
@@ -301,7 +271,7 @@ class Institution:
                 "termName": self.display_name,
                 "@type": "https://schema.org/Organization"
             }
-            return PrimitiveMetadataField("authorAffiliation", False, self.ror, expanded_value)
+            return PrimitiveMetadataField("authorAffiliation", False, self.ror, expanded_value=expanded_value)
         else:
             return PrimitiveMetadataField("authorAffiliation", False, self.display_name)
 
@@ -316,14 +286,12 @@ class Person:
         orcid (str): ORCID identifier (optional).
         email (str): Email address (optional).
         affiliation (Institution): Affiliation of the person (optional).
-        project (list[str]): List of associated projects.
     """
     family_name: str
     given_name: str
     orcid: str = ""
     email: str = ""
     affiliation: Institution | str = ""
-    project: list[str] = field(default_factory=list)
 
     def to_dict(self) -> dict[str, str | list[str] | dict[str, str]]:
             """
@@ -340,8 +308,7 @@ class Person:
                 "family_name": self.family_name,
                 "given_name": self.given_name,
                 "orcid": self.orcid,
-                "email": self.email,
+                "email": self.email
-                "project": self.project
             }
 
             if isinstance(self.affiliation, Institution):
@@ -464,12 +431,10 @@ class ConfigData:
 
     Attributes:
         dataverse (dict[str, str]): Dataverse-related configuration.
-        phase (dict[str, dict[str, int]]): Mapping of project phases.
         pis (list[dict[str, Any]]): List of principal investigator configurations.
         default_grants (list[dict[str, str]]): Default grant configurations.
     """
     dataverse: dict[str, str]
-    phase: dict[str, dict[str, int]]
     pis: list[dict[str, Any]]
     default_grants: list[dict[str, str]]
 
@@ -523,7 +488,6 @@ class Config:
 
         cls._config_data = ConfigData(
             dataverse=config_data.get('dataverse', {}),
-            phase=config_data.get('phase', {}),
             pis=config_data.get('pis', []),
             default_grants=config_data.get('default_grants', [])
         )
@@ -545,16 +509,6 @@ class Config:
             raise RuntimeError("Failed to load configuration")
         return cls._config_data
 
-    @property
-    def PHASE(self) -> dict[str, dict[str, int]]:
-        """
-        Get phase configuration.
-
-        Returns:
-            dict[str, dict[str, int]]: Mapping of phases.
-        """
-        return self.get_config().phase
-
     @property
     def PIS(self) -> list[dict[str, Any]]:
         """
@@ -833,7 +787,10 @@ class AbstractProcessor:
             else:
                 console.print(f"\n{ICONS['warning']} No abstract found in CrossRef!", style="warning")
         else:
+            if license.name:
                 console.print(f"\n{ICONS['info']} License {license.name} does not allow derivative works. Reconstructing abstract from OpenAlex!", style="info")
+            else:
+                console.print(f"\n{ICONS['info']} Custom license does not allow derivative works. Reconstructing abstract from OpenAlex!", style="info")
 
 
         openalex_abstract = self._get_openalex_abstract(data)
@@ -1406,8 +1363,7 @@ class MetadataProcessor:
                             CompoundMetadataField("grantNumber", True, grants).to_dict()
                         ],
                         "displayName": "Citation Metadata"
-                    },
+                    }
-                    "crc1430_org_v1": self._build_organization_metadata(data)
                 },
                 "files": []
             }
@@ -1473,71 +1429,22 @@ class MetadataProcessor:
         """
         return data.get("publication_year", "")
 
-    def _build_organization_metadata(self, data: dict[str, Any]) -> dict[str, Any]:
-        """
-        Build organization metadata fields (phase, project, PI names).
 
-        Args:
-            data (dict[str, Any]): The metadata.
-
-        Returns:
-            dict[str, Any]: Organization metadata.
-        """
-        publication_year = self._get_publication_year(data)
-        if publication_year:
-            phases = self._get_phases(int(publication_year))
-        else:
-            phases = []
-
-        pis = self._get_involved_pis(data)
-        projects: list[str] = []
-        for pi in pis:
-            for project in pi.project:
-                projects.append(project)
-
-        pi_names: list[str] = []
-        for pi in pis:
-            pi_names.append(pi.format_name())
-
-        # Deduplicate projects and PI names
-        unique_projects = list(set(projects))
-        unique_pi_names = list(set(pi_names))
-
-        return {
-            "fields": [
-                ControlledVocabularyMetadataField("crc1430OrgV1Phase", True, phases).to_dict(),
-                ControlledVocabularyMetadataField("crc1430OrgV1Project", True, unique_projects).to_dict(),
-                ControlledVocabularyMetadataField("crc1430OrgV1PI", True, unique_pi_names).to_dict()
-            ]
-        }
-
-    def _get_phases(self, year: int) -> list[str]:
-        """
-        Determine the project phases matching a given publication year.
-
-        Args:
-            year (int): The publication year.
-
-        Returns:
-            list[str]: List of matching phase names.
-        """
-        config = Config()
-        matching_phases: list[str] = []
-        for phase_name, phase_info in config.PHASE.items():
-            phase = Phase(phase_name, phase_info["start"], phase_info["end"])
-            if phase.check_year(year):
-                matching_phases.append(phase.name)
-        return matching_phases
 
     def _get_involved_pis(self, data: dict[str, Any]) -> list[Person]:
         """
-        Identify involved principal investigators from the metadata.
+        Identify involved principal investigators from the metadata for use as fallback
+        corresponding authors.
+
+        This method matches authors in the publication metadata against the configured
+        PIs and returns matching PIs. It is used as a fallback when no corresponding
+        authors are explicitly declared in the publication metadata.
 
         Args:
-            data (dict[str, Any]): The metadata.
+            data (dict[str, Any]): The metadata from OpenAlex.
 
         Returns:
-            list[Person]: List of PIs.
+            list[Person]: List of matching PIs for use as corresponding authors.
         """
         involved_pis: list[Person] = []
         for authorship in data.get("authorships", []):

tests/config_test.yaml

@@ -1,23 +1,16 @@
-default_grant:
+default_grants:
   - funder: "Awesome Funding Agency"
     id: "ABC12345"
 
-phase:
-  "Phase 1 (2021/2025)":
-    start: 2021
-    end: 2025
-
 pis:
   - family_name: "Doe"
     given_name: "Jon"
     orcid: "0000-0000-0000-0000"
     email: "jon.doe@iana.org"
     affiliation: "Institute of Science, Some University"
-    project: ["Project A01"]
 
   - family_name: "Doe"
     given_name: "Jane"
     orcid: "0000-0000-0000-0001"
     email: "jane.doe@iana.org"
     affiliation: "Institute of Science, Some University"
-    project: ["Project A02"]

tests/test_citation_builder.py

@@ -1,13 +1,9 @@
 import json
 import os
-import pytest
-from unittest.mock import MagicMock
 
-from doi2dataset import (
+import pytest
-    CitationBuilder,
+
-    PIFinder,
+from doi2dataset import CitationBuilder, Person, PIFinder
-    Person
-)
 
 
 @pytest.fixture
@@ -27,8 +23,7 @@ def test_pi():
         given_name="Author",
         orcid="0000-0000-0000-1234",
         email="test.author@example.org",
-        affiliation="Test University",
+        affiliation="Test University"
-        project=["Test Project"]
     )
 
 

tests/test_doi2dataset.py

@@ -3,21 +3,9 @@ import sys
 
 sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "..")))
 
-from doi2dataset import NameProcessor, Phase, sanitize_filename, validate_email_address
+from doi2dataset import NameProcessor, sanitize_filename, validate_email_address
 
 
-def test_phase_check_year():
-    """Test that check_year correctly determines if a year is within the phase boundaries."""
-    phase = Phase("TestPhase", 2000, 2010)
-    # Within boundaries
-    assert phase.check_year(2005) is True
-    # Outside boundaries
-    assert phase.check_year(1999) is False
-    assert phase.check_year(2011) is False
-    # Boundary cases
-    assert phase.check_year(2000) is True
-    assert phase.check_year(2010) is True
-
 def test_sanitize_filename():
     """Test the sanitize_filename function to convert DOI to a valid filename."""
     doi = "10.1234/abc.def"

tests/test_fetch_doi_mock.py

@@ -8,12 +8,11 @@ from doi2dataset import (
     APIClient,
     CitationBuilder,
     Config,
-    License,
     LicenseProcessor,
     MetadataProcessor,
     Person,
     PIFinder,
-    SubjectMapper
+    SubjectMapper,
 )
 
 
@@ -158,8 +157,7 @@ def test_pi_finder_find_by_orcid():
         given_name="Jon",
         orcid="0000-0000-0000-0000",
         email="jon.doe@iana.org",
-        affiliation="Institute of Science, Some University",
+        affiliation="Institute of Science, Some University"
-        project=["Project A01"]
     )
 
     # Create PIFinder with our test PI

tests/test_metadata_processor.py

@@ -1,7 +1,8 @@
 import json
 import os
+from unittest.mock import MagicMock
+
 import pytest
-from unittest.mock import MagicMock, patch
 
 from doi2dataset import MetadataProcessor
 
@@ -40,7 +41,6 @@ def test_build_metadata_basic_fields(metadata_processor, openalex_data, monkeypa
     # Mock methods that might cause issues in isolation
     metadata_processor._build_description = MagicMock(return_value="Test description")
     metadata_processor._get_involved_pis = MagicMock(return_value=[])
-    metadata_processor._build_organization_metadata = MagicMock(return_value={})
 
     # Call the method we're testing
     metadata = metadata_processor._build_metadata(openalex_data)
@@ -81,7 +81,6 @@ def test_build_metadata_authors(metadata_processor, openalex_data, monkeypatch):
     # Mock methods that might cause issues in isolation
     metadata_processor._build_description = MagicMock(return_value="Test description")
     metadata_processor._get_involved_pis = MagicMock(return_value=[])
-    metadata_processor._build_organization_metadata = MagicMock(return_value={})
 
     # Call the method we're testing
     metadata = metadata_processor._build_metadata(openalex_data)
@@ -130,7 +129,6 @@ def test_build_metadata_keywords_and_topics(metadata_processor, openalex_data, m
     # Mock methods that might cause issues in isolation
     metadata_processor._build_description = MagicMock(return_value="Test description")
     metadata_processor._get_involved_pis = MagicMock(return_value=[])
-    metadata_processor._build_organization_metadata = MagicMock(return_value={})
 
     # Call the method we're testing
     metadata = metadata_processor._build_metadata(openalex_data)

tests/test_person.py

@@ -1,5 +1,5 @@
-import pytest
+from doi2dataset import Institution, Person
-from doi2dataset import Person, Institution
+
 
 def test_person_to_dict_with_string_affiliation():
     """Test Person.to_dict() with a string affiliation."""
@@ -8,8 +8,7 @@ def test_person_to_dict_with_string_affiliation():
         given_name="John",
         orcid="0000-0001-2345-6789",
         email="john.doe@example.org",
-        affiliation="Test University",
+        affiliation="Test University"
-        project=["Project A"]
     )
 
     result = person.to_dict()
@@ -18,7 +17,6 @@ def test_person_to_dict_with_string_affiliation():
     assert result["given_name"] == "John"
     assert result["orcid"] == "0000-0001-2345-6789"
     assert result["email"] == "john.doe@example.org"
-    assert result["project"] == ["Project A"]
     assert result["affiliation"] == "Test University"
 
 
@@ -31,8 +29,7 @@ def test_person_to_dict_with_institution_ror():
         given_name="John",
         orcid="0000-0001-2345-6789",
         email="john.doe@example.org",
-        affiliation=inst,
+        affiliation=inst
-        project=["Project A"]
     )
 
     result = person.to_dict()