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rdhyee merged 1 commit into from
Oct 31, 2025
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Implement Eric Kansa's authoritative iSamples queries in Cesium tutorial #29

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250 changes: 196 additions & 54 deletions tutorials/parquet_cesium.qmd
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Original file line number Diff line number Diff line change
Expand Up @@ -343,57 +343,190 @@ async function get_samples_at_geo_cord_location_via_sample_event(pid) {
if (pid === null || pid ==="" || pid == "unset") {
return [];
}
// Eric Kansa's authoritative query from open-context-py
// Source: https://github.com/ekansa/open-context-py/blob/staging/opencontext_py/apps/all_items/isamples/isamples_explore.py
const q = `
-- Path 1: Direct event location
SELECT DISTINCT
s.pid as sample_pid,
s.label as sample_label,
s.name as sample_name,
event.label as event_label,
event.pid as event_pid,
site.label as site_label,
site.pid as site_pid,
'direct_event_location' as location_path
FROM nodes s
JOIN nodes e1 ON s.row_id = e1.s AND e1.p = 'produced_by'
JOIN nodes event ON e1.o[1] = event.row_id
JOIN nodes e2 ON event.row_id = e2.s AND e2.p = 'sample_location'
JOIN nodes g ON e2.o[1] = g.row_id
LEFT JOIN nodes e3 ON event.row_id = e3.s AND e3.p = 'sampling_site'
LEFT JOIN nodes site ON e3.o[1] = site.row_id
WHERE s.otype = 'MaterialSampleRecord'
AND event.otype = 'SamplingEvent'
AND g.otype = 'GeospatialCoordLocation'
AND g.pid = ?
SELECT
geo.latitude,
geo.longitude,
site.label AS sample_site_label,
site.pid AS sample_site_pid,
samp.pid AS sample_pid,
samp.alternate_identifiers AS sample_alternate_identifiers,
samp.label AS sample_label,
samp.description AS sample_description,
samp.thumbnail_url AS sample_thumbnail_url,
samp.thumbnail_url IS NOT NULL as has_thumbnail
FROM nodes AS geo
JOIN nodes AS rel_se ON (
rel_se.p = 'sample_location'
AND
list_contains(rel_se.o, geo.row_id)
)
JOIN nodes AS se ON (
rel_se.s = se.row_id
AND
se.otype = 'SamplingEvent'
)
JOIN nodes AS rel_site ON (
se.row_id = rel_site.s
AND
rel_site.p = 'sampling_site'
)
JOIN nodes AS site ON (
rel_site.o[1] = site.row_id
AND
site.otype = 'SamplingSite'
)
JOIN nodes AS rel_samp ON (
rel_samp.p = 'produced_by'
AND
list_contains(rel_samp.o, se.row_id)
)
JOIN nodes AS samp ON (
rel_samp.s = samp.row_id
AND
samp.otype = 'MaterialSampleRecord'
)
WHERE geo.pid = ?
AND geo.otype = 'GeospatialCoordLocation'
ORDER BY has_thumbnail DESC
`;
const result = await loadData(q, [pid], "loading_combined", "samples_combined");
return result ?? [];
}

UNION
async function get_sample_data_via_sample_pid(sample_pid) {
if (sample_pid === null || sample_pid === "" || sample_pid === "unset") {
return null;
}
// Eric Kansa's query: Get full sample data including geo and site info
const q = `
SELECT
samp.row_id,
samp.pid AS sample_pid,
samp.alternate_identifiers AS sample_alternate_identifiers,
samp.label AS sample_label,
samp.description AS sample_description,
samp.thumbnail_url AS sample_thumbnail_url,
samp.thumbnail_url IS NOT NULL as has_thumbnail,
geo.latitude,
geo.longitude,
site.label AS sample_site_label,
site.pid AS sample_site_pid
FROM nodes AS samp
JOIN nodes AS samp_rel_se ON (
samp_rel_se.s = samp.row_id
AND
samp_rel_se.p = 'produced_by'
)
JOIN nodes AS se ON (
samp_rel_se.o[1] = se.row_id
AND
se.otype = 'SamplingEvent'
)
JOIN nodes AS geo_rel_se ON (
geo_rel_se.s = se.row_id
AND
geo_rel_se.p = 'sample_location'
)
JOIN nodes AS geo ON (
geo_rel_se.o[1] = geo.row_id
AND
geo.otype = 'GeospatialCoordLocation'
)
JOIN nodes AS site_rel_se ON (
site_rel_se.s = se.row_id
AND
site_rel_se.p = 'sampling_site'
)
JOIN nodes AS site ON (
site_rel_se.o[1] = site.row_id
AND
site.otype = 'SamplingSite'
)
WHERE samp.pid = ?
AND samp.otype = 'MaterialSampleRecord'
`;
const result = await loadData(q, [sample_pid], "loading_sample_data", "sample_data");
return result && result.length ? result[0] : null;
}

-- Path 2: Via site location
SELECT DISTINCT
s.pid as sample_pid,
s.label as sample_label,
s.name as sample_name,
event.label as event_label,
event.pid as event_pid,
site.label as site_label,
site.pid as site_pid,
'via_site_location' as location_path
FROM nodes s
JOIN nodes e1 ON s.row_id = e1.s AND e1.p = 'produced_by'
JOIN nodes event ON e1.o[1] = event.row_id
JOIN nodes e2 ON event.row_id = e2.s AND e2.p = 'sampling_site'
JOIN nodes site ON e2.o[1] = site.row_id
JOIN nodes e3 ON site.row_id = e3.s AND e3.p = 'site_location'
JOIN nodes g ON e3.o[1] = g.row_id
WHERE s.otype = 'MaterialSampleRecord'
AND event.otype = 'SamplingEvent'
AND site.otype = 'SamplingSite'
AND g.otype = 'GeospatialCoordLocation'
AND g.pid = ?
async function get_sample_data_agents_sample_pid(sample_pid) {
if (sample_pid === null || sample_pid === "" || sample_pid === "unset") {
return [];
}
// Eric Kansa's query: Get agent info (who collected/registered)
const q = `
SELECT
samp.row_id,
samp.pid AS sample_pid,
samp.alternate_identifiers AS sample_alternate_identifiers,
samp.label AS sample_label,
samp.description AS sample_description,
samp.thumbnail_url AS sample_thumbnail_url,
samp.thumbnail_url IS NOT NULL as has_thumbnail,
agent_rel_se.p AS predicate,
agent.pid AS agent_pid,
agent.name AS agent_name,
agent.alternate_identifiers AS agent_alternate_identifiers
FROM nodes AS samp
JOIN nodes AS samp_rel_se ON (
samp_rel_se.s = samp.row_id
AND
samp_rel_se.p = 'produced_by'
)
JOIN nodes AS se ON (
samp_rel_se.o[1] = se.row_id
AND
se.otype = 'SamplingEvent'
)
JOIN nodes AS agent_rel_se ON (
agent_rel_se.s = se.row_id
AND
list_contains(['responsibility', 'registrant'], agent_rel_se.p)
)
JOIN nodes AS agent ON (
list_contains(agent_rel_se.o, agent.row_id)
AND
agent.otype = 'Agent'
)
WHERE samp.pid = ?
AND samp.otype = 'MaterialSampleRecord'
`;
const result = await loadData(q, [sample_pid], "loading_agents", "agents");
return result ?? [];
}

ORDER BY sample_label
async function get_sample_types_and_keywords_via_sample_pid(sample_pid) {
if (sample_pid === null || sample_pid === "" || sample_pid === "unset") {
return [];
}
// Eric Kansa's query: Get classification keywords and types
const q = `
SELECT
samp.row_id,
samp.pid AS sample_pid,
samp.alternate_identifiers AS sample_alternate_identifiers,
samp.label AS sample_label,
kw_rel.p AS predicate,
kw.pid AS keyword_pid,
kw.label AS keyword
FROM nodes AS samp
JOIN nodes AS kw_rel ON (
kw_rel.s = samp.row_id
AND
list_contains(['keywords', 'has_sample_object_type', 'has_material_category'], kw_rel.p)
)
JOIN nodes AS kw ON (
list_contains(kw_rel.o, kw.row_id)
AND
kw.otype = 'IdentifiedConcept'
)
WHERE samp.pid = ?
AND samp.otype = 'MaterialSampleRecord'
`;
const result = await loadData(q, [pid, pid], "loading_combined", "samples_combined");
const result = await loadData(q, [sample_pid], "loading_keywords", "keywords");
return result ?? [];
}

Expand Down Expand Up @@ -691,18 +824,27 @@ ${JSON.stringify(samples_2, null, 2)}
```


## Combined Samples at Location (Path 1 + Path 2 with Rich Metadata)
## Samples at Location via Sampling Event (Eric Kansa's Query)

<div id="loading_combined" hidden>Loading samples…</div>

This query implements Eric Kansa's authoritative `get_samples_at_geo_cord_location_via_sample_event` function from [open-context-py](https://github.com/ekansa/open-context-py/blob/staging/opencontext_py/apps/all_items/isamples/isamples_explore.py).

<div id="loading_combined" hidden>Loading combined samples…</div>
**Query Strategy (Path 1 Only)**:
- Starts at a GeospatialCoordLocation (clicked point)
- Walks **backward** via `sample_location` edges to find SamplingEvents that reference this location
- From those events, finds MaterialSampleRecords produced by them
- Requires site context (INNER JOIN on `sampling_site` → SamplingSite)

This query implements Eric Kansa's `get_samples_at_geo_cord_location_via_sample_event` function, which combines both Path 1 and Path 2 using UNION and returns sample metadata including:
**Returns**:
- Geographic coordinates: `latitude`, `longitude`
- Sample metadata: `sample_pid`, `sample_label`, `sample_description`, `sample_alternate_identifiers`
- Site context: `sample_site_label`, `sample_site_pid`
- Media: `sample_thumbnail_url`, `has_thumbnail`

- Sample metadata: `sample_pid`, `sample_label`, `sample_name`
- Event context: `event_label`, `event_pid`
- Site information: `site_label`, `site_pid` (when available via Path 2)
- Path indicator: `location_path` (direct_event_location or via_site_location)
**Ordering**: Prioritizes samples with images (`ORDER BY has_thumbnail DESC`)

Results are ordered alphabetically by sample label.
**Important**: This query only returns samples whose **sampling events directly reference this geolocation** via `sample_location` (Path 1). Samples that reach this location only through their site's `site_location` (Path 2) are **not included**. This means site marker locations may return 0 results if no events were recorded at that exact coordinate.

```{ojs}
//| echo: false
Expand Down