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Dataplotter partition #292

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9932fb3
add autocommit flag
steve-fischer-200 Nov 12, 2025
b875ebe
Merge branch 'master' into sqlutils-autocommit
steve-fischer-200 Nov 12, 2025
64506d1
change default to ares13
steve-fischer-200 Dec 11, 2025
ddee302
use org_abbrev
steve-fischer-200 Jan 22, 2026
db51f3f
merge from master
steve-fischer-200 Feb 6, 2026
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27 changes: 9 additions & 18 deletions ...ice/src/main/java/org/apidb/apicommon/service/services/dataPlotter/ProfileSetService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -45,14 +45,16 @@ FETCH_SIZE, new ResultSetToJsonConverter()),
}

@GET
@Path("TranscriptionSummaryProfiles/{sourceId}")
@Path("TranscriptionSummaryProfiles/{orgAbbrev}/{sourceId}")
@Produces(MediaType.APPLICATION_JSON)
public Response getTranscriptionSummaryProfiles(
@PathParam("orgAbbrev") String orgAbbrev,
@PathParam("sourceId") String sourceId)
throws WdkModelException {
String projectId = getWdkModel().getProjectId();
String sql = DataPlotterQueries.getQueryMap(projectId).get("transcription_summary_profiles");
sql = sql.replaceAll("\\$id", sourceId);
sql = sql.replaceAll("\\$orgAbbrev", orgAbbrev);
return getStreamingResponse(sql,
"getTranscriptionSummaryProfiles", "Failed running SQL to fetch transcription summary profile set names.");
}
Expand Down Expand Up @@ -160,11 +162,11 @@ public Response getCompoundPeaksIdentifierAmoB(




@GET
@Path("GutherCategory/{sourceId}")
@Path("GutherCategory/{orgAbbrev}/{sourceId}")
@Produces(MediaType.APPLICATION_JSON)
public Response getGutherCategory(
@PathParam("orgAbbrev") String orgAbbrev,
@PathParam("sourceId") String sourceId)
throws WdkModelException {
String sql = " SELECT nfe.categorical_value AS cat_val" +
Expand All @@ -184,6 +186,7 @@ public Response getGutherCategory(
" AND i.external_database_release_id = r.external_database_release_id" +
" AND r.external_database_id = d.external_database_id" +
" AND d.NAME ='tbruTREU927_quantitative_massSpec_Guther_glycosomal_proteome_RSRC'" +
" AND ga.orgAbbrev = '" + orgAbbrev + "'" +
" AND ga.gene_source_id = '" + sourceId + "'";
return getStreamingResponse(sql,
"getGutherCategory", "Failed running SQL to fetch Guther dataset category.");
Expand All @@ -205,6 +208,8 @@ public Response getPlotData(
for (int i = 0; i < profileSets.length(); i++) {
JSONObject profileSet = profileSets.getJSONObject(i);
String id = new String();
String orgAbbrev = profileSet.has("orgAbbrev")?
profileSet.getString("orgAbbrev") : "no_org_abbrev";
if (profileSet.has("idOverride")) {
id = profileSet.getString("idOverride");
} else {
Expand Down Expand Up @@ -268,10 +273,10 @@ public Response getPlotData(
plotDataSql = plotDataSql + " order by profile_order, element_order";
}

plotDataSql = plotDataSql.replaceAll("\\$orgAbbrev", orgAbbrev);
return getStreamingResponse(plotDataSql,
"plotData", "Failed running SQL to fetch plot data.");
}

private String getProfileSetSql(String projectId, String profileSetName, String profileType, String sourceId, String displayName, int order) {

String colsToReturn = order + " as profile_order, name, value, samplenames.profile_set_name, samplenames.profile_type, samplenames.element_order";
Expand Down Expand Up @@ -299,18 +304,6 @@ private String getProfileSetByECSql(String projectId, String profileSetName, Str
return sql;
}

private String getProfileSetWithMetadataSql(String projectId, String profileSetName, String profileType, String facet, String xAxis, String sourceId, int order) {

String sql = DataPlotterQueries.getQueryMap(projectId).get("profile_set_with_metadata");
sql = sql.replaceAll("\\$order", Integer.toString(order));
sql = sql.replaceAll("\\$profileSetName", profileSetName);
sql = sql.replaceAll("\\$profileType", profileType);
sql = sql.replaceAll("\\$sourceId", sourceId);
sql = sql.replaceAll("\\$facet", facet);
sql = sql.replaceAll("\\$xAxis", xAxis);

return sql;
}

private String getProfileSetNamesSql(String projectId, String datasetPresenterId, String sourceId) {
String sql = sourceId.equals("none")
Expand Down Expand Up @@ -391,8 +384,6 @@ private String getSql(String projectId, String sqlName, String param1, String pa
return getProfileSetNamesSql(projectId, param1, param2);
case "Profile":
return getProfileSetSql(projectId, param1, param2, param3, param4, order);
case "ProfileWithMetadata":
return getProfileSetWithMetadataSql(projectId, param1, param2, param3, param4, param5, order);
case "RankedNthSourceIdNames":
return getRankedValuesSql(projectId, sqlName, param1, param2, param3, param4, order);
case "RankedNthValues":
Expand Down