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Session Continuity Notes - Oct 3, 2025

Current Status: Phase 2 Complete ✅

We're in the middle of integrating Eric Kansa's 4 query functions from oc_parquet_analysis_enhanced.ipynb into /tutorials/parquet_cesium.qmd.

Completed Work

Phase 1: Documentation (Commit d5d6690)

  • ✅ Added comprehensive Path 1/Path 2 explanation with diagrams
  • ✅ Added full relationship map (Agent, IdentifiedConcept paths)
  • ✅ Added Eric's 4 query function analysis with summary table

Phase 2: First Query Implementation (Commit 3224eb1)

  • ✅ Implemented get_samples_at_geo_cord_location_via_sample_event()
  • ✅ Combines Path 1 + Path 2 with UNION
  • ✅ Returns rich metadata: thumbnail_url, description, alternate_identifiers, site info
  • ✅ Added reactive cell selectedSamplesCombined with loading state
  • ✅ Added display section "Combined Samples at Location"

What's Next: Phase 3

Remaining 2 queries from Eric's notebook (cell 59):

  1. Agent Query - get_sample_data_agents_sample_pid(sample_pid)

    • Shows who collected/registered samples
    • Path: MaterialSampleRecord → produced_by → SamplingEvent → {responsibility, registrant} → Agent
    • Returns: sample metadata + agent info (agent_pid, agent_name, predicate)
    • Note: Independent of Path 1/Path 2 (no geographic data needed)

  2. Keywords/Concepts Query - get_sample_types_and_keywords_via_sample_pid(sample_pid)

    • Shows material types and classifications
    • Path: MaterialSampleRecord → {keywords, has_sample_object_type, has_material_category} → IdentifiedConcept
    • Returns: sample metadata + concept info (keyword_pid, keyword, predicate)
    • Note: Direct edges to concepts, bypasses SamplingEvent entirely!

Key Technical Details

Table alias difference:

  • Eric's Python notebook uses: FROM pqg AS ...
  • Our JavaScript implementation uses: FROM nodes ...
  • DuckDB view is created as: CREATE VIEW nodes AS SELECT * FROM read_parquet('${parquet_path}')

Loading pattern to follow:

async function get_FUNCTION_NAME(pid) {
    if (pid === null || pid ==="" || pid == "unset") return [];
    const q = `SQL QUERY HERE`;
    const result = await loadData(q, [pid], "loading_ID", "key");
    return result ?? [];
}

mutable FUNCTIONLoading = false;

selectedFUNCTION = {
    mutable FUNCTIONLoading = true;
    try {
        return await get_FUNCTION_NAME(clickedPointId);
    } finally {
        mutable FUNCTIONLoading = false;
    }
}

Display pattern:

## Section Title

<div id="loading_ID" hidden>Loading message…</div>

Explanation text...

\`\`\`{ojs}
//| echo: false
variable = selectedFUNCTION
FUNCTIONLoading ? md`(loading…)` : md`\`\`\`
${JSON.stringify(variable, null, 2)}
\`\`\`
`
\`\`\`

File Locations

Main working file: /Users/raymondyee/C/src/iSamples/isamplesorg.github.io/tutorials/parquet_cesium.qmd

Reference notebook: /Users/raymondyee/C/src/iSamples/isamples-python/examples/basic/oc_parquet_analysis_enhanced.ipynb (cell 59)

Local parquet: http://localhost:4979/assets/oc_isamples_pqg.parquet (691MB, in docs/assets/)

Branch: issue-13-parquet-duckdb

Quick Start Commands

# Navigate to project
cd /Users/raymondyee/C/src/iSamples/isamplesorg.github.io

# Check current branch
git status

# Start Quarto preview (if needed)
quarto preview

# View notebook for reference
code /Users/raymondyee/C/src/iSamples/isamples-python/examples/basic/oc_parquet_analysis_enhanced.ipynb

Session Pickup Prompt

"Let's continue integrating Eric's queries into parquet_cesium.qmd. We completed Phase 2 (combined samples query). Next we need to add the agent query and keywords/concepts query. Should we start with the agent query?"

Notes

  • All existing queries (get_samples_1, get_samples_2, get_samples_at_geo_cord_location_via_sample_event) are working and preserved
  • Pattern is established - just need to adapt Eric's remaining 2 SQL queries to JavaScript
  • Consider UI improvements after Phase 3 complete (tables, clickable links, thumbnails)