From 8a678e69189838d9456885687668a199e7c02d26 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Wed, 21 Jan 2026 15:11:31 -0500 Subject: [PATCH 1/2] adjust dataplotter query --- Model/lib/xml/dataPlotter/queries.xml | 4 +++- blig | 11 +++++++++++ 2 files changed, 14 insertions(+), 1 deletion(-) create mode 100644 blig diff --git a/Model/lib/xml/dataPlotter/queries.xml b/Model/lib/xml/dataPlotter/queries.xml index b50dff120..3be1d3f62 100644 --- a/Model/lib/xml/dataPlotter/queries.xml +++ b/Model/lib/xml/dataPlotter/queries.xml @@ -51,7 +51,7 @@ diff --git a/blig b/blig new file mode 100644 index 000000000..a6fedaea4 --- /dev/null +++ b/blig @@ -0,0 +1,11 @@ +ec_number_gene, pathway_id + +gene_source_id + +gene_source_id, ec_number_gene, pathway_id + +pathway_id + +complete_ec, exact_match, ext_db_rls, pathway_source_id, pathway_source, gene_source_id, ec_number_gene, ec_number_pathway + +gene_source_id, complete_ec, exact_patch, pathway_source \ No newline at end of file From d28eba09a56a28fcc96e851a37cea580b24fdc9e Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Thu, 22 Jan 2026 19:06:12 -0500 Subject: [PATCH 2/2] use org_abbrev in dataplotter --- Model/lib/xml/dataPlotter/queries.xml | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/Model/lib/xml/dataPlotter/queries.xml b/Model/lib/xml/dataPlotter/queries.xml index 3be1d3f62..403a39fea 100644 --- a/Model/lib/xml/dataPlotter/queries.xml +++ b/Model/lib/xml/dataPlotter/queries.xml @@ -8,7 +8,7 @@ ', ' || dsp.short_attribution, '''', '`') as display_name, dsp.dataset_presenter_id as presenter_id, ds.order_num - from apidbTuning.Profile p, + from apidbTuning.Profile_p p, apidbTuning.ProfileSamples ps, study.ProtocolAppNode pan, apidbtuning.datasetdatasource dd, @@ -23,6 +23,7 @@ and p.dataset_subtype = 'rnaseq' and p.profile_type = 'values' and p.source_id = '$id' + and p.org_abbrev = '$orgAbbrev' and ((dprop.value = 'false' and pan.name like '%firststrand%') or (dprop.value = 'true' @@ -72,7 +73,7 @@ @@ -97,7 +99,7 @@ (select max(rownum) as m from($sourceIdValueQuery)) ct where ('$sourceId' = 'ALL' AND (rn = 1 or rn = ct.m or mod(rn, round(ct.m/$N,0)) = 0)) - OR '$sourceId' = source_id + OR ('$sourceId' = source_id and '$orgAbbrev' = org_abbrev) ]]> @@ -133,8 +135,9 @@ from (select row_number() OVER () as rn, points.* from ( ( select row_number() OVER () as rn, vs.* from ( SELECT profile_study_id, dataset_name, p.profile_set_name, p.profile_type, p.node_type, unnest( STRING_TO_ARRAY(p.profile_AS_STRING, chr(9) ,'')) as oneval - FROM apidbtuning.Profile p + FROM apidbtuning.Profile_p p where p.profile_type = 'values' + AND p.org_abbrev = '$orgAbbrev' AND p.profile_set_name || ' [' || node_type || ']' = '$profileSetName' ) vs ) vals @@ -173,6 +176,7 @@ and pts.profile_study_id = vals.profile_study_id AND ec.ec_number LIKE REPLACE(REPLACE(REPLACE(REPLACE(lower('$sourceId'),' ',''),'-', '%'),'*','%'),'any','%')) ec WHERE p.profile_set_name || ' [' || node_type || ']' = '$profileSetName' AND p.profile_type = '$profileType' + AND p.org_abbrev = '$orgAbbrev' AND p.source_id = ec.gene_source_id) t , table(cast(multiset(select level from dual connect by level <= length (regexp_replace(t.profile_as_string, '[^' || CHR(9) || ']+')) + 1) as sys.OdciNumberList)) levels) samplevalues where samplenames.element_order = samplevalues.element_order @@ -248,6 +252,7 @@ and pts.profile_study_id = vals.profile_study_id and ps.profile_type = 'values' and ps.protocol_app_node_id = na.protocol_app_node_id and na.na_feature_id = ga.na_feature_id + and ga.org_abbrev='$orgAbbrev', and ga.source_id='$sourceId') sense_comp , (select ps.node_order_num, ps.protocol_app_node_name , na.value @@ -258,6 +263,7 @@ and pts.profile_study_id = vals.profile_study_id and ps.profile_type = 'values' and ps.protocol_app_node_id = na.protocol_app_node_id and na.na_feature_id = ga.na_feature_id + and ga.org_abbrev='$orgAbbrev', and ga.source_id='$sourceId') sense_ref where sense_comp.protocol_app_node_name != sense_ref.protocol_app_node_name) sense , (select antisense_ref.protocol_app_node_name || '->' || antisense_comp.protocol_app_node_name as name @@ -270,6 +276,7 @@ and pts.profile_study_id = vals.profile_study_id and ps.profile_type = 'values' and ps.protocol_app_node_id = na.protocol_app_node_id and na.na_feature_id = ga.na_feature_id + and ga.org_abbrev='$orgAbbrev', and ga.source_id='$sourceId') antisense_comp , (select ps.node_order_num,ps.protocol_app_node_name,na.value from apidbtuning.ProfileSamples ps @@ -279,7 +286,8 @@ and pts.profile_study_id = vals.profile_study_id and ps.profile_type = 'values' and ps.protocol_app_node_id = na.protocol_app_node_id and na.na_feature_id = ga.na_feature_id - and ga.source_id='$sourceId') antisense_ref + and ga.org_abbrev='$orgAbbrev', + and ga.source_id='$sourceId') antisense_ref where antisense_comp.protocol_app_node_name != antisense_ref.protocol_app_node_name) antisense where sense.name = antisense.name ]]>