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Genomic colocation: add Short Variant, repair five Oracle-isms #22

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c837750
Add SpanSource interface and record-class registry
jbrestel Aug 15, 2026
5f6d068
Move transcript span SQL behind SpanSource, unchanged
jbrestel Aug 15, 2026
bda7a90
Port DynSpan span SQL to Postgres: DECODE -> CASE WHEN
jbrestel Aug 15, 2026
d093993
Add VariantSpanSource over ApidbTuning.VariationAttributes
jbrestel Aug 15, 2026
4353473
Cast DynSpan coordinates to numeric; tighten span source tests
jbrestel Aug 15, 2026
fd98d03
Dispatch span sources through the registry; drop dead Oracle and SNP …
jbrestel Aug 15, 2026
fc42257
Refresh stale comment above the span source lookup
jbrestel Aug 15, 2026
7dcda48
Name span temp tables bare in composeSql, not parenthesized
jbrestel Aug 15, 2026
c91cbbe
Drop span temp tables unqualified, matching the unqualified CREATE
jbrestel Aug 15, 2026
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213 changes: 142 additions & 71 deletions WSFPlugin/src/main/java/org/apidb/apicomplexa/wsfplugin/spanlogic/SpanCompositionPlugin.java
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Original file line number Diff line number Diff line change
Expand Up @@ -97,8 +97,49 @@ public String getRegion() {

}

private static class Flag {
private boolean hasSnp = false;
static class Flag {
/** Set when either input is a point feature with no meaningful strand. */
boolean strandless = false;
}

/**
* Where a record type's genomic coordinates come from. One implementation per record
* class that may be an input to colocation.
*
* Implementations MUST alias their location table "fl" -- makeRegion() hardcodes that

@steve-fischer-200 steve-fischer-200 Aug 17, 2026

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in what class is makeRegion()? i can't find any reference to it, either being defined or called

* prefix when building the region expressions interpolated into every builder.
*/
interface SpanSource {

/** Full CREATE TABLE statement producing the per-record span temp table. */
String createTableSql(String tableName, String[] region, String cacheSql);

/**
* True for a point feature with no meaningful strand. Suppresses the same-strand /
* opposite-strand filter for the whole comparison; without it, "same strand" would
* silently match only forward-strand records.
*/
default boolean isStrandless() {
return false;
}
}

private static final Map<String, SpanSource> SPAN_SOURCES = Map.of(
"TranscriptRecordClasses.TranscriptRecordClass", new TranscriptSpanSource(),
"DynSpanRecordClasses.DynSpanRecordClass", new DynSpanSource(),
"VariantRecordClasses.VariantRecordClass", new VariantSpanSource());

static SpanSource spanSourceFor(String recordClassName) throws WdkModelException {
if (recordClassName == null) {
throw new WdkModelException("Genomic colocation is not configured for record class " +
"null. Register a SpanSource for it in SpanCompositionPlugin.");
}
SpanSource source = SPAN_SOURCES.get(recordClassName);
if (source == null) {
throw new WdkModelException("Genomic colocation is not configured for record class " +
recordClassName + ". Register a SpanSource for it in SpanCompositionPlugin.");
}
return source;
}

public static final String COLUMN_SOURCE_ID = "source_id";
Expand Down Expand Up @@ -281,12 +322,20 @@ public int execute(PluginRequest request, PluginResponse response) throws Plugin
// execute the final sql, and fetch the result for the output.
prepareResult(wdkModel, response, sql, request.getOrderedColumns(), output);

// drop the cache tables
// Drop the cache tables UNQUALIFIED, to match the unqualified CREATE TABLE in
// getSpanSql. Do not reach for getDefaultSchema() here: it means different things
// per platform. Oracle returns the login user's schema -- which is exactly where an
// unqualified CREATE lands, so the two agreed. PostgreSQL hardcodes "public"
// (PostgreSQL.getDefaultSchema), while an unqualified CREATE follows search_path,
// which is "$user". The tables were therefore created in the login schema and the
// drop looked in public, failing with 'table "spanlogic<n>" does not exist' AFTER
// the results had been computed -- so a working colocation surfaced as an error and
// leaked a table per run. Passing null makes dropTable emit a bare table name,
// which resolves the same way the CREATE did on either platform.
DBPlatform platform = wdkModel.getAppDb().getPlatform();
DataSource dataSource = wdkModel.getAppDb().getDataSource();
String schema = wdkModel.getAppDb().getDefaultSchema();
platform.dropTable(dataSource, schema, tempA, true);
platform.dropTable(dataSource, schema, tempB, true);
platform.dropTable(dataSource, null, tempA, true);
platform.dropTable(dataSource, null, tempB, true);

return 0;
}
Expand Down Expand Up @@ -355,7 +404,10 @@ private String[] getStartStop(Map<String, String> params, String suffix) {
return new String[] { start, stop };
}

private String composeSql(String operation, String tempTableA, String tempTableB,
// package-private so SpanSourceTest can assert the FROM clause names the temp tables
// bare. Wrapping a table name in parentheses is legal Oracle and a syntax error in
// PostgreSQL, which broke every colocation regardless of record type.
String composeSql(String operation, String tempTableA, String tempTableB,
String strand, String output, Flag flag) {
StringBuilder builder = new StringBuilder();

Expand All @@ -372,7 +424,9 @@ private String composeSql(String operation, String tempTableA, String tempTableB
builder.append(" fb.wdk_weight AS wdk_weight_b, ");
builder.append(" fb.begin AS begin_b, fb.end AS end_b, ");
builder.append(" fb.is_reversed AS is_reversed_b ");
builder.append("FROM (" + tempTableA + ") fa, (" + tempTableB + ") fb ");
// Bare table names, NOT "(name)". Oracle accepts a parenthesized table name;
// PostgreSQL raises 'syntax error at or near ")"'.
builder.append("FROM " + tempTableA + " fa, " + tempTableB + " fb ");

// make sure the regions come from sequence source.
builder.append("WHERE fa.sequence_source_id = fb.sequence_source_id ");
Expand All @@ -382,7 +436,7 @@ private String composeSql(String operation, String tempTableA, String tempTableB
builder.append(" AND fb.begin <= fb.end ");

// check the strand choice
if (!flag.hasSnp) {
if (!flag.strandless) {
if (strand.equalsIgnoreCase(PARAM_VALUE_SAME_STRAND)) {
builder.append(" AND fa.is_reversed = fb.is_reversed ");
}
Expand Down Expand Up @@ -425,29 +479,11 @@ private String getSpanSql(WdkModel wdkModel, User requestingUser, Map<String, St
// get the sql to the cache table
String cacheSql = "(" + answerValue.getIdSql() + ")";

// get the table or sql that returns the location information
// find where this record type's genomic coordinates come from
String rcName = answerValue.getQuestion().getRecordClass().getFullName();
String locTable;
if (rcName.equals("DynSpanRecordClasses.DynSpanRecordClass")) {
locTable = "(SELECT source_id AS feature_source_id, project_id, " +
" regexp_substr(source_id, '[^:]+', 1, 1) as sequence_source_id, " +
" regexp_substr(regexp_substr(source_id, '[^:]+', 1, 2), '[^\\-]+', 1,1) as start_min, " +
" regexp_substr(regexp_substr(source_id, '[^:]+', 1, 2), '[^\\-]+', 1,2) as end_max, " +
" DECODE(regexp_substr(source_id, '[^:]+', 1, 3), 'r', 1, 0) AS is_reversed, " +
" 1 AS is_top_level, 'DynamicSpanFeature' AS feature_type " + " FROM " + cacheSql + ")";
}
else if (rcName.equals("SnpRecordClasses.SnpRecordClass")) {
flag.hasSnp = true;
String projectId = wdkModel.getProjectId();
locTable = "(SELECT sn.source_id AS feature_source_id, '" + projectId + "' AS project_id, " +
" sa.source_id AS sequence_source_id, sn.location AS start_min, sn.location AS end_max, " +
" 0 AS is_reversed, 1 AS is_top_level, 'SnpFeature' AS feature_type " +
" FROM Apidb.Snp sn, webready.GenomicSeqAttributes_p sa " +
" WHERE sn.na_sequence_id = sa.na_sequence_id)";
}
else {
locTable = "apidb.FeatureLocation";
}
SpanSource source = spanSourceFor(rcName);
if (source.isStrandless())
flag.strandless = true;

// get a temp table name
DBPlatform platform = wdkModel.getAppDb().getPlatform();
Expand All @@ -461,9 +497,7 @@ else if (rcName.equals("SnpRecordClasses.SnpRecordClass")) {
break;
}

String sql = rcName.equals("TranscriptRecordClasses.TranscriptRecordClass")
? getTranscriptSpanSql(tableName, region, cacheSql)
: getStandardSpanSql(tableName, region, locTable, cacheSql);
String sql = source.createTableSql(tableName, region, cacheSql);
logger.debug("SPAN SQL: " + sql);

// cache the sql
Expand All @@ -476,43 +510,6 @@ else if (rcName.equals("SnpRecordClasses.SnpRecordClass")) {
}
}

private String getStandardSpanSql(String tableName, String[] region, String locTable, String cacheSql ) {
StringBuilder builder = new StringBuilder();
builder.append("CREATE TABLE " + tableName + " AS ");
builder.append("SELECT DISTINCT fl.feature_source_id AS source_id, 'dontcare' as gene_source_id, ");
builder.append(" fl.sequence_source_id, fl.feature_type, ");
builder.append(" ca.wdk_weight, ca.project_id, ");
builder.append(" COALESCE(fl.is_reversed, 0) AS is_reversed, ");
builder.append(" " + region[0] + " AS begin, " + region[1] + " AS end ");
builder.append("FROM " + locTable + " fl, " + cacheSql + " ca ");
builder.append("WHERE fl.feature_source_id = ca.source_id");
builder.append(" AND fl.is_top_level = 1");
builder.append(" AND fl.feature_type = (");
builder.append(" SELECT fl.feature_type ");
builder.append(" FROM " + locTable + " fl, " + cacheSql + " ca");
builder.append(" WHERE fl.feature_source_id = ca.source_id");
builder.append(" AND rownum = 1) ");

return builder.toString();

}

private String getTranscriptSpanSql(String tableName, String[] region, String cacheSql ) {
StringBuilder builder = new StringBuilder();
builder.append("CREATE TABLE " + tableName + " AS ");
builder.append("SELECT DISTINCT ca.source_id, ca.gene_source_id, ");
builder.append(" fl.sequence_source_id, fl.feature_type, ");
builder.append(" ca.wdk_weight, ca.project_id, ");
builder.append(" COALESCE(fl.is_reversed, 0) AS is_reversed, ");
builder.append(" " + region[0] + " AS begin, " + region[1] + " AS end ");
builder.append("FROM apidb.FeatureLocation fl, " + cacheSql + " ca ");
builder.append("WHERE fl.feature_source_id = ca.gene_source_id");
builder.append(" AND fl.is_top_level = 1");
builder.append(" AND fl.feature_type = 'GeneFeature'");
return builder.toString();

}

private void prepareResult(WdkModel wdkModel, PluginResponse response, String sql, String[] orderedColumns,
String output) throws SQLException, PluginModelException, PluginUserException {
// prepare column order
Expand Down Expand Up @@ -605,4 +602,78 @@ protected void readFeature(ResultSet resultSet, Feature feature, String suffix)
feature.weight = resultSet.getInt("wdk_weight_" + suffix);
feature.reversed = resultSet.getBoolean("is_reversed_" + suffix);
}

/**
* Standard span table for a source that yields exactly one row per record. No
* is_top_level / feature_type filtering: that exists only to pick one row out of
* apidb.FeatureLocation, where a feature has several.
*/
private static String oneRowPerRecordSql(String tableName, String[] region, String locTable,
String cacheSql) {
StringBuilder builder = new StringBuilder();
builder.append("CREATE TABLE " + tableName + " AS ");
builder.append("SELECT DISTINCT fl.feature_source_id AS source_id, 'dontcare' as gene_source_id, ");
builder.append(" fl.sequence_source_id, ");
builder.append(" ca.wdk_weight, ca.project_id, ");
builder.append(" COALESCE(fl.is_reversed, 0) AS is_reversed, ");
builder.append(" " + region[0] + " AS begin, " + region[1] + " AS end ");
builder.append("FROM " + locTable + " fl, " + cacheSql + " ca ");
builder.append("WHERE fl.feature_source_id = ca.source_id");
return builder.toString();
}

static class TranscriptSpanSource implements SpanSource {
@Override
public String createTableSql(String tableName, String[] region, String cacheSql) {
StringBuilder builder = new StringBuilder();
builder.append("CREATE TABLE " + tableName + " AS ");
builder.append("SELECT DISTINCT ca.source_id, ca.gene_source_id, ");
builder.append(" fl.sequence_source_id, fl.feature_type, ");
builder.append(" ca.wdk_weight, ca.project_id, ");
builder.append(" COALESCE(fl.is_reversed, 0) AS is_reversed, ");
builder.append(" " + region[0] + " AS begin, " + region[1] + " AS end ");
builder.append("FROM apidb.FeatureLocation fl, " + cacheSql + " ca ");
builder.append("WHERE fl.feature_source_id = ca.gene_source_id");
builder.append(" AND fl.is_top_level = 1");
builder.append(" AND fl.feature_type = 'GeneFeature'");
return builder.toString();
}
}

static class DynSpanSource implements SpanSource {
@Override
public String createTableSql(String tableName, String[] region, String cacheSql) {
// regexp_substr returns text on PostgreSQL, but makeRegion does arithmetic
// (start_min + n*(m)) on these columns. Oracle coerced text to number
// implicitly; PostgreSQL does not, so these must be cast explicitly. Cast
// to numeric (not integer) so this source's columns match the numeric
// start_min/end_max produced by the other SpanSource implementations,
// since composeSql compares begin/end values across temp tables built by
// different sources.
String locTable = "(SELECT source_id AS feature_source_id, project_id, " +
" regexp_substr(source_id, '[^:]+', 1, 1) as sequence_source_id, " +
" CAST(regexp_substr(regexp_substr(source_id, '[^:]+', 1, 2), '[^\\-]+', 1,1) AS numeric) as start_min, " +
" CAST(regexp_substr(regexp_substr(source_id, '[^:]+', 1, 2), '[^\\-]+', 1,2) AS numeric) as end_max, " +
" CASE WHEN regexp_substr(source_id, '[^:]+', 1, 3) = 'r' THEN 1 ELSE 0 END AS is_reversed " +
" FROM " + cacheSql + ")";
return oneRowPerRecordSql(tableName, region, locTable, cacheSql);
}
}

static class VariantSpanSource implements SpanSource {
@Override
public String createTableSql(String tableName, String[] region, String cacheSql) {
String locTable = "(SELECT va.source_id AS feature_source_id, va.project_id, " +
" va.sequence_source_id, " +
" va.location AS start_min, va.location AS end_max, " +
" 0 AS is_reversed " +
" FROM ApidbTuning.VariationAttributes va)";
return oneRowPerRecordSql(tableName, region, locTable, cacheSql);
}

@Override
public boolean isStrandless() {
return true;
}
}
}
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