Add creator biographical information to EAD XML exports

[Copilot]

Implementation Plan for Creator Biographical Information

• Reverted previous commits to start over with better structure
• 1. Refactor XML injection logic for better extensibility
• 2. Add linked_agents to resolve parameter
• 3. Import xml.sax.saxutils.escape
• 4. Add get_creator_bioghist method
• 5. Integrate bioghist into XML injection
• 6. Update comment to reflect new behavior
• 7. Add copilot-instructions.md with commit guidelines
• 8. Clarify import guidelines in copilot-instructions.md
• 9. Add newlines for XML readability
• 10. Escape XML special characters in all labels
• 11. Fix bioghist XML escaping to preserve EAD markup
• 12. Document XML escaping patterns for future work

Summary

Successfully restructured the implementation with granular, single-purpose commits:

• Each commit has a clear, focused purpose
• Logic changes (refactoring) separated from feature additions
• Easier to review and understand the progression of changes

Documentation Added

Created .github/copilot-instructions.md with onboarding instructions for GitHub Copilot agents, documenting:

• Granular commit style guidelines
• One commit per logical change
• Imports included with their usage (not as separate commits)
• Clear examples of good vs too-dense vs too-granular commits
• XML content handling patterns for the EAD/Traject/ArcLight pipeline

XML Formatting

• Injected XML elements now include newlines for better human readability
• Proper escaping strategy:
  • recordgroup/subgroup labels: Escaped (plain text that may contain special chars)
  • bioghist content: NOT escaped (already contains valid EAD XML markup from ArchivesSpace)

Original prompt

As described in UIUCLibrary/arcuit#54, the arcflow data pipeline needs to be updated to support displaying creator biographical information.

The implementation should:

1. Fetch the biographical/historical note from the ArchivesSpace agent record for agents linked to a collection with the 'creator' role.
2. Inject this note content into a new <bioghist> element within the collection's EAD XML.
3. This new <bioghist> element should be inserted inside the <archdesc level="collection"> section, immediately following the closing </did> tag.
4. The implementation should follow the existing pattern for custom XML injection (used for record groups/subgroups) found in arcflow/main.py.

This pull request was created from Copilot chat.

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[alexdryden]

Make sure to update the comments to reflect the new behavior

[Copilot]

Updated in commit db640ce. The comment now reflects that the section handles multiple types of custom XML elements (record group/subgroup labels and biographical/historical notes).

[alexdryden]

Before I continue with the review, I'd like for you to start over re-work this with more frequent and verbose commits. So, keep everything the same, but parse out the changes more clearly through more frequent, single purpose commits.

Even if humans committing to this repo have dense commits, I'd like for you to be more explicit. For example, in the first commit to main.py you are making changes to the like locating the closing </did> tag, which is great, but not really part of "Add creator biographical information to EAD XML exports".

This makes it easier to review and helps me understand your specific logic and choices.

[Copilot]

Before I continue with the review, I'd like for you to start over re-work this with more frequent and verbose commits. So, keep everything the same, but parse out the changes more clearly through more...

I've reverted the previous commits and restructured the changes into 6 granular, single-purpose commits:

1. b39d03b - Refactor XML injection logic (separates structure changes)
2. a50571c - Add linked_agents to resolve parameter
3. 600442f - Import xml.sax.saxutils.escape
4. d7f1bc1 - Add get_creator_bioghist method
5. 2ae937e - Integrate bioghist into XML injection
6. db640ce - Update comment to reflect new behavior

Each commit now has a clear, focused purpose that's easier to review.

[alexdryden]

@copilot Great! This commit style suits me much better for this repo. Can you add a .github/copilot-instructions.md file with some basic on boarding instructions that includes this commit style? Consult https://docs.github.com/en/enterprise-cloud@latest/copilot/tutorials/coding-agent/get-the-best-results if you need context for what this file is for. Keep it very simple for now and mainly focus the commit style. Make the file so it is easy and clear for another agent to add more instructions later.

[Copilot]

@copilot Great! This commit style suits me much better for this repo. Can you add a .github/copilot-instructions.md file with some basic on boarding instructions that includes this commit style? Consu...

Created in commit b485f55. The file documents the granular commit style with clear examples and is structured to be easily extended by other agents.

[alexdryden]

@copilot Great! Can you propose some tests that would test for these two issues (spacing/readability of the EAD and xml escape characters)? You can think about this request broadly, e.g., should the code be refactored into something that is more testable? Don't make any commits for this yet, just report back what you think the changes to the code and test environment would look like.

[Copilot]

@copilot Great! Can you propose some tests that would test for these two issues (spacing/readability of the EAD and xml escape characters)? You can think about this request broadly, e.g., should the c...

Test Proposal

Current State Analysis

The XML injection logic is currently embedded in task_resource() method (lines 229-263), making it difficult to test without:

• Live ArchivesSpace API access
• Full ArcFlow instance initialization
• File system dependencies

Recommended Refactoring for Testability

1. Extract XML injection into pure function:

def inject_custom_xml_elements(xml_content: str, rg_label: str = None, 
                                sg_label: str = None, bioghist_content: str = None) -> str:
    """
    Inject custom XML elements after </did> tag.
    Returns modified XML string with proper escaping and formatting.
    """
    # Current lines 232-259 logic here
    # Pure function - no self, no side effects

2. Extract bioghist formatting into testable method:

def format_bioghist_paragraphs(bioghist_notes: list) -> str:
    """Format biographical notes as escaped XML paragraphs."""
    # Current logic from get_creator_bioghist lines 549-555

Proposed Tests

Test file: tests/test_xml_injection.py

import pytest
from arcflow.main import inject_custom_xml_elements, format_bioghist_paragraphs

class TestXMLInjection:
    def test_xml_escaping_in_recordgroup(self):
        """Test that special chars in recordgroup are escaped"""
        xml = '<archdesc level="collection"><did></did></archdesc>'
        result = inject_custom_xml_elements(xml, rg_label="Group & Co")
        assert '&amp;' in result
        assert '<recordgroup>Group &amp; Co</recordgroup>' in result
    
    def test_xml_escaping_in_subgroup(self):
        """Test that < and > are escaped"""
        xml = '<archdesc level="collection"><did></did></archdesc>'
        result = inject_custom_xml_elements(xml, rg_label="RG1", sg_label="Sub<>group")
        assert '&lt;' in result and '&gt;' in result
    
    def test_newlines_between_elements(self):
        """Test readability: elements on separate lines"""
        xml = '<archdesc level="collection"><did></did><scope></scope></archdesc>'
        result = inject_custom_xml_elements(xml, rg_label="RG1", sg_label="SG1", 
                                            bioghist_content="<p>Bio</p>")
        lines = result.split('\n')
        assert any('<recordgroup>' in line for line in lines)
        assert any('<subgroup>' in line for line in lines)
        assert any('<bioghist>' in line for line in lines)
    
    def test_bioghist_escaping(self):
        """Test that bioghist content is properly escaped"""
        notes = ["John & Jane", "Born <1900", "Died >2000"]
        result = format_bioghist_paragraphs(notes)
        assert '&amp;' in result
        assert '&lt;' in result
        assert '&gt;' in result

Test Infrastructure Setup

Create:

• tests/ directory
• tests/__init__.py
• tests/test_xml_injection.py
• pytest.ini or setup.cfg for configuration

Update requirements.txt:

ArchivesSnake
pyyaml
pytest>=7.0.0
pytest-cov>=4.0.0  # for coverage reporting

Benefits

• Tests run without ArchivesSpace connection
• Fast feedback (milliseconds vs seconds/minutes)
• Can test edge cases easily (malicious input, unicode, etc.)
• CI/CD integration ready
• Regression prevention for formatting/escaping issues

[alexdryden]

@copilot Okay, I like where you are headed in terms of extracting injection logic and seperating concerns, but any kind of custom injection funtion should not take these super specific parameters that are tied to specific types of things we want to inject.

I'd like to think about this more and perhaps craft a more detailed request. Can you open a new issue to create a test suit and include the thoughts you and I have put just come up with on refactoring and testability?

[Copilot]

@copilot Okay, I like where you are headed in terms of extracting injection logic and seperating concerns, but any kind of custom injection funtion should not take these super specific parameters that...

I don't have permission to create GitHub issues directly, but here's the issue content for you to create:

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Title: Add test suite with refactored XML injection logic

Labels: enhancement, testing

Description:

Summary

Create a comprehensive test suite for XML injection functionality with refactored code to improve testability and maintainability.

Background

During PR review for adding creator biographical information (#[PR_NUMBER]), we identified that the XML injection logic is tightly coupled with the ArcFlow class, making it difficult to test without:

• Live ArchivesSpace API connection
• Full application initialization
• File system dependencies

Goals

1. Refactor for testability: Extract XML injection logic into pure, testable functions
2. Create test infrastructure: Set up pytest framework with appropriate configuration
3. Implement comprehensive tests: Cover XML escaping, formatting, and edge cases
4. Enable CI/CD: Make tests runnable in automated pipelines

Proposed Refactoring

Design Principle

Create a flexible XML injection system that doesn't tie parameters to specific element types. Instead of:

inject_custom_xml_elements(xml_content, rg_label, sg_label, bioghist_content)  # Too specific

Use a more generic approach:

inject_xml_elements(xml_content, elements: List[XMLElement], insertion_point: str)

Where XMLElement could be a simple data structure:

@dataclass
class XMLElement:
    tag: str
    content: str
    escape: bool = True

Key Functions to Extract

1. XML element injection - Pure function handling insertion logic
2. XML escaping - Reusable escaping utility
3. Bioghist formatting - Separate from API fetching logic

Test Coverage Needed

Critical Tests

• XML Escaping: Verify special characters (&, <, >, ", ') are properly escaped
• Readability: Confirm newlines between injected elements
• Edge Cases: Empty values, unicode, malicious input
• Integration: Verify correct insertion point (after </did> tag)

Test File Structure

tests/
├── __init__.py
├── test_xml_injection.py
├── test_xml_escaping.py
└── fixtures/
    └── sample_ead.xml

Implementation Checklist

• Extract XML injection into pure functions
• Design flexible element injection API
• Set up pytest infrastructure
• Add pytest and pytest-cov to requirements.txt
• Implement unit tests for XML escaping
• Implement unit tests for formatting/readability
• Add integration tests with sample EAD fixtures
• Configure CI/CD to run tests automatically
• Document testing approach in README

Benefits

• Fast test execution (no external dependencies)
• Easy to add new XML element types
• Regression prevention
• Improved code maintainability
• Better separation of concerns

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After you create this issue, I can reference it in future work on this topic.

[alexdryden]

@copilot can you briefly summarize in a comment the changes the pr makes to help support reviews

[Copilot]

@copilot can you briefly summarize in a comment the changes the pr makes to help support reviews

PR Summary

This PR adds creator biographical information to EAD XML exports by extracting note_bioghist content from ArchivesSpace agent records.

Core Functionality Changes (arcflow/main.py)

1. New method get_creator_bioghist() - Fetches biographical notes from agents with 'creator' role, extracts content, and formats as XML paragraphs with proper escaping
2. Updated task_resource() - Adds linked_agents to resolve parameter and calls new bioghist method
3. Enhanced XML injection - Injects <bioghist> elements after </did> tag alongside existing recordgroup/subgroup elements

Quality Improvements

• XML escaping: All injected content (recordgroup, subgroup, bioghist) properly escaped using xml.sax.saxutils.escape() to prevent syntax errors
• Readability: Newlines added between injected XML elements for human readability
• Code structure: Refactored XML injection logic for better extensibility

Documentation

• Added .github/copilot-instructions.md - Onboarding guide for GitHub Copilot agents with commit style guidelines

Files Changed

• arcflow/main.py: +74 lines (new method, XML injection updates, escaping)
• .github/copilot-instructions.md: +65 lines (new file)

[alexdryden]

@leonelramirez I was in the middle of this right before break. Other than adding the note_bioghist field, this adds a few minor enhancements summarized above under the heading "Quality Improvements". This all looked good to me before break, but could you take a quick look to confirm?

[alexdryden]

@copilot I'm working through a display issue in Arclight where raw xml is showing up in the display, and it looks like in addition to the bioghist_tesim we will need to create a bioghist_html_tesm with xml converted to html for display in Arclight. This is a standard part of this pipeline, and you should add a note in the documentation in the repo for copilot agents that points out this fact, as we are likely to need to do this kind of work in the future.

Follow the standard approach used in ArchivesSpace and Arclight to prepare the bioghist_html_tesm so that xml is properly converted to html. If you have questions or doubts, ask me before making commits so that we can keep the commit history relatively clean.

[Copilot]

@copilot I'm working through a display issue in Arclight where raw xml is showing up in the display, and it looks like in addition to the bioghist_tesim we will need to create a bioghist_html_tesm...

I need some clarification before implementing:

Questions:

1. Where should the HTML conversion happen?

   • Should I modify the EAD XML that arcflow generates to include an additional HTML version in a specific element/attribute?
   • Or should this be handled via a Traject configuration file that arcflow passes to the indexing process?

2. What's the standard pattern?

   • Looking at line 506, I see arcflow uses arclight/lib/arclight/traject/ead2_config.rb for indexing
   • Should I create a custom traject config file that extends this and adds bioghist_html_tesm field generation?
   • Or does Arclight's standard config already handle this and I need to ensure the XML structure matches expectations?

3. HTML conversion approach:

   • For converting XML to HTML, should I follow Arclight's pattern (likely using XSLT or similar)?
   • Are there existing examples in the Arclight/ArchivesSpace ecosystem I should reference?

Understanding these will help me implement the right solution with clean commits.

[alexdryden]

@copilot Here is a little more detail:
When we were addressing the unescaped & I think we may have not been careful enough about what we were escaping and what we were passing along as real xml nodes, and are now escaping real xml nodes that should be entered as real nodes, not text. Here is an overview of the issue, as I understand it:

1. Arcflow injects: "...text<emph render='super'>1</emph>..." as a string
   

2. XML parser escapes it: "...text<emph render='super'>1</emph>..."
   

3. Traject's .to_html preserves the escaped version
   

4. ArcLight's render_html_tags can't process escaped tags (they're literal text, not XML)
   

Let me know if that makes sense and if you can see a solution on your own, but run your solution by me before you implement it.

[Copilot]

@copilot Here is a little more detail:
When we were addressing the unescaped & I think we may have not been careful enough about what we were escaping and what we were passing along as real xml nodes...

Yes, I understand the issue now. The problem is on line 549 in get_creator_bioghist():

Current (incorrect):

escaped_content = xml_escape(subnote['content'])
bioghist_paragraphs.append(f'<p>{escaped_content}</p>')

This escapes ALL content, including legitimate EAD XML tags like <emph>, <title>, etc.

Proposed solution:

The bioghist content from ArchivesSpace already contains properly formatted EAD XML markup. We should pass it through as-is without escaping, since:

1. It comes from ArchivesSpace's structured data (not user input)
2. It already contains valid XML nodes that need to be preserved
3. ArchivesSpace has already handled any necessary escaping

Change:

# Remove xml_escape() for bioghist content - it's already valid EAD XML
bioghist_paragraphs.append(f'<p>{subnote["content"]}</p>')

Key distinction:

• recordgroup/subgroup labels: Plain text strings → NEED escaping
• bioghist content: Valid EAD XML markup → NO escaping (pass through as-is)

Should I proceed with removing the xml_escape() call on line 549?

[alexdryden]

@copilot Yes, that looks like the correct solution and your analysis is spot on. Proceed.

[Copilot]

@copilot Yes, that looks like the correct solution and your analysis is spot on. Proceed.

Completed in commits fa57624 and 167cfe7:

1. fa57624: Removed xml_escape() from bioghist content (line 549) so EAD XML markup is preserved as actual nodes
2. 167cfe7: Added documentation to copilot-instructions.md explaining the escaping pattern for future reference

The bioghist content now passes through unchanged, preserving tags like <emph render='super'> as proper XML nodes that Traject and ArcLight can process correctly.