From 8b5a1072842306a3ab0d9c15ab79f9dd18b9ff3a Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Tue, 9 Dec 2025 10:34:58 -0500 Subject: [PATCH 01/66] fix tuning table syntax errors --- Model/lib/xml/tuningManager/apiTuningManager.xml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml index 42d8cba58..b7c2e2767 100644 --- a/Model/lib/xml/tuningManager/apiTuningManager.xml +++ b/Model/lib/xml/tuningManager/apiTuningManager.xml @@ -1588,14 +1588,14 @@ create index Organism_projectId_idx&1 ON OrganismAttributes&1 (project_id, sourc @@ -2313,7 +2313,7 @@ create index Organism_projectId_idx&1 ON OrganismAttributes&1 (project_id, sourc - + Text for PreferredProduct table on gene record page. @@ -2453,7 +2453,7 @@ create index Organism_projectId_idx&1 ON OrganismAttributes&1 (project_id, sourc - + all products for each gene From 46f440f53489a7a9d0c1e593d3fbd4234e59a07d Mon Sep 17 00:00:00 2001 From: Steve <43149795+steve-fischer-200@users.noreply.github.com> Date: Tue, 9 Dec 2025 12:25:51 -0500 Subject: [PATCH 02/66] fix intronjunction queries (#130) --- .../model/questions/params/organismParams.xml | 2 +- .../model/questions/queries/geneQueries.xml | 15 ++++++---- .../model/questions/queries/spanQueries.xml | 19 +++++++----- .../records/junctionAttributeQueries.xml | 6 ++-- Model/lib/xml/jbrowse/genomeQueries.xml | 30 +++++++++---------- 5 files changed, 39 insertions(+), 33 deletions(-) diff --git a/Model/lib/wdk/model/questions/params/organismParams.xml b/Model/lib/wdk/model/questions/params/organismParams.xml index 1a88a696c..8438fe595 100644 --- a/Model/lib/wdk/model/questions/params/organismParams.xml +++ b/Model/lib/wdk/model/questions/params/organismParams.xml @@ -391,7 +391,7 @@ WITH FilterQuery AS ( SELECT DISTINCT ga.organism, ga.org_abbrev - FROM apidbtuning.geneintronjunction gij, apidbtuning.GeneAttributes ga + FROM webready.geneintronjunction_p gij, apidbtuning.GeneAttributes ga WHERE ga.source_id = gij.gene_source_id ) /* end filter query */ diff --git a/Model/lib/wdk/model/questions/queries/geneQueries.xml b/Model/lib/wdk/model/questions/queries/geneQueries.xml index 4b3d7b36a..842b89d16 100644 --- a/Model/lib/wdk/model/questions/queries/geneQueries.xml +++ b/Model/lib/wdk/model/questions/queries/geneQueries.xml @@ -2176,7 +2176,7 @@ , gij.total_unique , gij.total_isrpm , gij.annotated_intron - FROM apidbtuning.geneintronjunction gij, webready.TranscriptAttributes_p ga + FROM webready.geneintronjunction_p gij, webready.TranscriptAttributes_p ga WHERE ga.na_sequence_id = gij.na_sequence_id AND ( gij.segment_end BETWEEN ga.start_min - $$max_flanking_bp$$ AND ga.end_max + $$max_flanking_bp$$ @@ -2186,6 +2186,7 @@ AND gij.total_unique >= $$min_total_unique$$ AND gij.taxon_id = ga.taxon_id AND ga.org_abbrev IN ($$organism$$) + AND gij.org_abbrev IN ($$organism$$) ) , gmi AS ( SELECT gene_source_id, source_id, max(total_unique) AS max_unique, max(total_isrpm) AS max_isrpm FROM core @@ -2210,12 +2211,13 @@ = $$min_total_unique$$ AND gij.annotated_intron = 'No' AND gij.percent_max between $$percent_max.min$$ and $$percent_max.max$$ AND ga.org_abbrev in ($$organism$$) + AND gij.org_abbrev in ($$organism$$) AND gij.taxon_id = ga.taxon_id GROUP BY ga.gene_source_id, ga.source_id, ga.project_id ]]> @@ -3187,6 +3189,7 @@ + @@ -3218,8 +3221,8 @@ WHERE igi.bait_gene_feature_id = pf.gene_na_feature_id ) AS prey_number_of_baits, bait_number_of_preys, 'bait' AS bait_or_prey FROM webready.GeneId_p ga - , webready.TranscriptAttributes_p bf - , webready.TranscriptAttributes_p pf + , apidbtuning.TranscriptAttributes bf + , apidbtuning.TranscriptAttributes pf , apidb.GeneInteraction gi WHERE lower($$single_gene_id$$) = lower(ga.id) AND ga.gene = bf.gene_source_id AND gi.number_of_searches >= $$min_searches$$ AND gi.times_observed >= $$min_observed$$ AND @@ -3232,8 +3235,8 @@ WHERE igi.prey_gene_feature_id = bf.gene_na_feature_id ) AS bait_number_of_preys, 'prey' AS bait_or_prey FROM webready.GeneId_p ga - , webready.TranscriptAttributes_p bf - , webready.TranscriptAttributes_p pf + , apidbtuning.TranscriptAttributes bf + , apidbtuning.TranscriptAttributes pf , apidb.GeneInteraction gi WHERE lower($$single_gene_id$$) = lower(ga.id) AND ga.gene = pf.gene_source_id AND gi.number_of_searches >= $$min_searches$$ AND gi.times_observed >= $$min_observed$$ AND diff --git a/Model/lib/wdk/model/questions/queries/spanQueries.xml b/Model/lib/wdk/model/questions/queries/spanQueries.xml index 1529303f7..fd18021d1 100644 --- a/Model/lib/wdk/model/questions/queries/spanQueries.xml +++ b/Model/lib/wdk/model/questions/queries/spanQueries.xml @@ -194,11 +194,12 @@ select INTRON_FEATURE_ID as feature_id, gsa.project_id, ab.internal_abbrev, CONCAT(gij.sequence_source_id, ':', gij.segment_start, '-', gij.segment_end, CASE gij.is_reversed WHEN 0 THEN ':f' WHEN 1 THEN ':r' END) as source_id - from ApidbTuning.GeneIntronJunction gij, webready.GenomicSeqJunctionStats_p stats ,sres.taxonname tn ,webready.GenomicSeqAttributes_p gsa ,apidbtuning.organismattributes ab + from webready.GeneIntronJunction_p gij, webready.GenomicSeqJunctionStats_p stats ,sres.taxonname tn ,webready.GenomicSeqAttributes_p gsa ,apidbtuning.organismattributes ab WHERE gij.na_sequence_id = stats.na_sequence_id and gsa.taxon_id = tn.taxon_id and gsa.na_sequence_ID = gij.na_sequence_id and ab.organism_name = gsa.organism + and gij.org_abbrev in ($$organism_span$$) and gsa.org_abbrev in ($$organism_span$$) and stats.org_abbrev in ($$organism_span$$) AND gij.segment_end - gij.segment_start <= stats.max_intron_length * 2 @@ -229,19 +230,21 @@ select INTRON_FEATURE_ID as feature_id, and gsa.taxon_id = tn.taxon_id and gsa.na_sequence_ID = gij.na_sequence_id and ab.organism_name = gsa.organism + and gij.org_abbrev in ($$organism_span$$) and gsa.org_abbrev in ($$organism_span$$) and stats.org_abbrev in ($$organism_span$$) AND gij.segment_end - gij.segment_start <= stats.max_intron_length * 4 AND gij.total_unique >= CASE WHEN contained = 1 THEN stats.min_annot_score ELSE 5*stats.min_annot_score END AND (gij.contained = 0 or gij.percent_max >= stats.min_annot_percent_max) AND gij.intron_feature_id not in ( - select gij.intron_feature_id - from ApidbTuning.GeneIntronJunction gij, webready.GenomicSeqJunctionStats_p stats - WHERE gij.na_sequence_id = stats.na_sequence_id - AND gij.segment_end - gij.segment_start <= stats.max_intron_length * 2 - AND gij.total_unique >= CASE WHEN contained = 1 THEN stats.perc01_annot_score ELSE 5*stats.perc01_annot_score END - AND (gij.contained = 0 or gij.percent_max >= 2 /*stats.perc0005_annot_percent_max*/) - + select gij.intron_feature_id + from ApidbTuning.GeneIntronJunction gij, webready.GenomicSeqJunctionStats_p stats + WHERE gij.na_sequence_id = stats.na_sequence_id + AND gij.segment_end - gij.segment_start <= stats.max_intron_length * 2 + AND gij.total_unique >= CASE WHEN contained = 1 THEN stats.perc01_annot_score ELSE 5*stats.perc01_annot_score END + AND (gij.contained = 0 or gij.percent_max >= 2 /*stats.perc0005_annot_percent_max*/) + AND gij.org_abbrev in ($$organism_span$$) + AND stats.org_abbrev in ($$organism_span$$) ) ) where (confidence = $$Intron_junction_confidence$$ or 'all' = $$Intron_junction_confidence$$) diff --git a/Model/lib/wdk/model/records/junctionAttributeQueries.xml b/Model/lib/wdk/model/records/junctionAttributeQueries.xml index 09cc38b4f..469fe0351 100644 --- a/Model/lib/wdk/model/records/junctionAttributeQueries.xml +++ b/Model/lib/wdk/model/records/junctionAttributeQueries.xml @@ -60,7 +60,7 @@ --> - SELECT count(*) FROM ApidbTuning.GeneIntronJunction + SELECT count(*) FROM webready.GeneIntronJunction_p @@ -73,7 +73,7 @@ @@ -96,7 +96,7 @@ diff --git a/Model/lib/xml/jbrowse/genomeQueries.xml b/Model/lib/xml/jbrowse/genomeQueries.xml index c09172db3..38624e396 100644 --- a/Model/lib/xml/jbrowse/genomeQueries.xml +++ b/Model/lib/xml/jbrowse/genomeQueries.xml @@ -143,8 +143,8 @@ ORDER BY WHEN gij.is_reversed = 1 THEN '-1' ELSE '.' END AS strand - FROM ApidbTuning.GeneIntronJunction gij - JOIN ApidbTuning.GeneIntJuncStats stats + FROM webready.GeneIntronJunction_p gij + JOIN webready.GenomicSeqJunctionStats_p stats ON gij.na_sequence_id = stats.na_sequence_id where gij.parent_id = $srcfeature_id AND gij.segment_start <= $rend @@ -176,8 +176,8 @@ gij.annotated_intron, gij.annotated_intron as annotatedintron, gij.gene_source_i WHEN gij.is_reversed = 1 THEN '-1' ELSE '.' END AS strand - FROM ApidbTuning.GeneIntronJunction gij - JOIN ApidbTuning.GeneIntJuncStats stats + FROM webready.GeneIntronJunction_p gij + JOIN webready.GenomicSeqJunctionStats_p stats ON gij.na_sequence_id = stats.na_sequence_id where gij.na_sequence_id = $srcfeature_id AND gij.segment_start <= $rend @@ -202,8 +202,8 @@ gij.annotated_intron, gij.annotated_intron as annotatedintron, gij.gene_source_i WHEN gij.is_reversed = 1 THEN '-1' ELSE '.' END AS strand - FROM ApidbTuning.GeneIntronJunction gij - JOIN ApidbTuning.GeneIntJuncStats stats + FROM webready.GeneIntronJunction_p gij + JOIN webready.GenomicSeqJunctionStats_p stats ON gij.na_sequence_id = stats.na_sequence_id where gij.na_sequence_id= $srcfeature_id AND gij.segment_start <= $rend @@ -226,8 +226,8 @@ gij.annotated_intron, gij.annotated_intron as annotatedintron, gij.gene_source_i WHEN gij.is_reversed = 1 THEN '-1' ELSE '.' END AS strand - FROM ApidbTuning.GeneIntronJunction gij - JOIN ApidbTuning.GeneIntJuncStats stats + FROM webready.GeneIntronJunction_p gij + JOIN webready.GenomicSeqJunctionStats_p stats ON gij.na_sequence_id = stats.na_sequence_id where gij.na_sequence_id = $srcfeature_id AND gij.segment_start <= $rend @@ -252,8 +252,8 @@ gij.annotated_intron, gij.annotated_intron as annotatedintron, gij.gene_source_i WHEN gij.is_reversed = 1 THEN '-1' ELSE '.' END AS strand - FROM ApidbTuning.GeneIntronJunction gij - JOIN ApidbTuning.GeneIntJuncStats stats + FROM webready.GeneIntronJunction_p gij + JOIN webready.GenomicSeqJunctionStats_p stats ON gij.na_sequence_id = stats.na_sequence_id where gij.na_sequence_id = $srcfeature_id AND gij.segment_start <= $rend @@ -265,7 +265,7 @@ gij.annotated_intron, gij.annotated_intron as annotatedintron, gij.gene_source_i AND (gij.contained = 0 or gij.percent_max >= stats.min_annot_percent_max) AND gij.intron_feature_id not in ( select gij.intron_feature_id - from ApidbTuning.GeneIntronJunction gij, ApidbTuning.GeneIntJuncStats stats + from webready.GeneIntronJunction_p gij, webready.GenomicSeqJunctionStats_p stats where gij.na_sequence_id = $srcfeature_id AND gij.segment_start <= $rend AND gij.segment_end >= $base_start @@ -2645,7 +2645,7 @@ WHERE loc.na_sequence_id = $srcfeature_id ANNOTATED_INTRON, to_char(segment_start - 10) || ',' || to_char(segment_end + 1) as tstarts, to_char(10) || ',' || to_char(10) as blocksizes - from ApidbTuning.GeneIntronJunction gij, ApidbTuning.GeneIntJuncStats stats + from webready.GeneIntronJunction_p gij, webready.GenomicSeqJunctionStats_p stats where gij.na_sequence_id= $srcfeature_id AND gij.segment_start <= $rend AND gij.segment_end >= $base_start @@ -2671,7 +2671,7 @@ WHERE loc.na_sequence_id = $srcfeature_id ANNOTATED_INTRON, to_char(segment_start - 10) || ',' || to_char(segment_end + 1) as tstarts, to_char(10) || ',' || to_char(10) as blocksizes - from ApidbTuning.GeneIntronJunction gij, ApidbTuning.GeneIntJuncStats stats + from webready.GeneIntronJunction_p gij, webready.GenomicSeqJunctionStats_p stats where gij.na_sequence_id = $srcfeature_id AND gij.segment_start <= $rend AND gij.segment_end >= $base_start @@ -2698,7 +2698,7 @@ WHERE loc.na_sequence_id = $srcfeature_id ANNOTATED_INTRON, to_char(segment_start - 10) || ',' || to_char(segment_end + 1) as tstarts, to_char(10) || ',' || to_char(10) as blocksizes - from ApidbTuning.GeneIntronJunction gij, ApidbTuning.GeneIntJuncStats stats + from webready.GeneIntronJunction_p gij, webready.GenomicSeqJunctionStats_p stats where gij.na_sequence_id = $srcfeature_id AND gij.segment_start <= $rend AND gij.segment_end >= $base_start @@ -2710,7 +2710,7 @@ WHERE loc.na_sequence_id = $srcfeature_id AND (gij.contained = 0 or gij.percent_max >= stats.min_annot_percent_max) AND gij.intron_feature_id not in ( select gij.intron_feature_id - from ApidbTuning.GeneIntronJunction gij, ApidbTuning.GeneIntJuncStats stats + from webready.GeneIntronJunction_p gij, webready.GenomicSeqJunctionStats_p stats where gij.na_sequence_id = $srcfeature_id AND gij.segment_start <= $rend AND gij.segment_end >= $base_start From d305fea6d17c8fdf80ed5293ec396b4523c89717 Mon Sep 17 00:00:00 2001 From: Steve <43149795+steve-fischer-200@users.noreply.github.com> Date: Tue, 9 Dec 2025 12:29:59 -0500 Subject: [PATCH 03/66] avoid use of dots.nasequence (#128) --- .../model/questions/params/organismParams.xml | 10 ++++---- .../model/questions/queries/geneQueries.xml | 6 +++-- .../questions/queries/genomicQueries.xml | 9 +++---- .../model/records/genomicAttributeQueries.xml | 24 +++++++------------ 4 files changed, 20 insertions(+), 29 deletions(-) diff --git a/Model/lib/wdk/model/questions/params/organismParams.xml b/Model/lib/wdk/model/questions/params/organismParams.xml index 8438fe595..7de643449 100644 --- a/Model/lib/wdk/model/questions/params/organismParams.xml +++ b/Model/lib/wdk/model/questions/params/organismParams.xml @@ -639,9 +639,8 @@ /* withSequenceStrains filter query */ WITH FilterQuery AS ( SELECT DISTINCT sa.organism - FROM dots.NaSequence ns, apidbtuning.GenomicSeqAttributes sa, apidb.organism o - WHERE ns.na_sequence_id = sa.na_sequence_id - AND sa.taxon_id = o.taxon_id + FROM apidbtuning.GenomicSeqAttributes sa, apidb.organism o + WHERE sa.taxon_id = o.taxon_id AND (sa.project_id = '@PROJECT_ID@' OR 'UniDB' = '@PROJECT_ID@') ) /* end filter query */ @@ -699,9 +698,8 @@ /* withSequenceStrains filter query */ WITH FilterQuery AS ( SELECT DISTINCT sa.organism, o.abbrev - FROM dots.NaSequence ns, apidbtuning.GenomicSeqAttributes sa, apidb.organism o - WHERE ns.na_sequence_id = sa.na_sequence_id - AND sa.taxon_id = o.taxon_id + FROM apidbtuning.GenomicSeqAttributes sa, apidb.organism o + WHERE sa.taxon_id = o.taxon_id AND (sa.project_id = '@PROJECT_ID@' OR 'UniDB' = '@PROJECT_ID@') ) /* end filter query */ diff --git a/Model/lib/wdk/model/questions/queries/geneQueries.xml b/Model/lib/wdk/model/questions/queries/geneQueries.xml index 842b89d16..435016110 100644 --- a/Model/lib/wdk/model/questions/queries/geneQueries.xml +++ b/Model/lib/wdk/model/questions/queries/geneQueries.xml @@ -5196,9 +5196,10 @@ = $$start_point$$ AND (gene_start_min <= $$end_point$$ OR $$end_point$$ = 0) diff --git a/Model/lib/wdk/model/questions/queries/genomicQueries.xml b/Model/lib/wdk/model/questions/queries/genomicQueries.xml index 34ef543aa..1699b2631 100644 --- a/Model/lib/wdk/model/questions/queries/genomicQueries.xml +++ b/Model/lib/wdk/model/questions/queries/genomicQueries.xml @@ -68,10 +68,9 @@ @@ -327,12 +326,10 @@ , pan.name FROM apidb.chrcopynumber ccn , study.protocolappnode pan - , dots.nasequence ns , webready.GenomicSeqAttributes_p sa WHERE ccn.protocol_app_node_id in ($$CNV_strain$$) AND ccn.protocol_app_node_id = pan.protocol_app_node_id - AND ns.na_sequence_id = ccn.na_sequence_id - AND ns.source_id = sa.source_id + AND sa.na_sequence_id = ccn.na_sequence_id AND sa.chromosome IS NOT NULL ) , median AS ( diff --git a/Model/lib/wdk/model/records/genomicAttributeQueries.xml b/Model/lib/wdk/model/records/genomicAttributeQueries.xml index 0e7f0a6a8..6287c4e15 100644 --- a/Model/lib/wdk/model/records/genomicAttributeQueries.xml +++ b/Model/lib/wdk/model/records/genomicAttributeQueries.xml @@ -328,20 +328,20 @@ - SELECT ns.source_id, gs.project_id, - ns.source_id as gff_seqid, + SELECT gs.source_id, gs.project_id, + gs.source_id as gff_seqid, gs.project_id as gff_source, s.name as gff_type, 1 as gff_fstart, - ns.length as gff_fend, + gs.length as gff_fend, '.' as gff_score, '+' as gff_strand, '.' as gff_phase, - ns.source_id as gff_attr_id, - ns.source_id as gff_attr_web_id, - ns.source_id as gff_attr_name, - ns.description as gff_attr_description, - ns.length as gff_attr_size, + gs.source_id as gff_attr_id, + gs.source_id as gff_attr_web_id, + gs.source_id as gff_attr_name, + gs.sequence_description as gff_attr_description, + gs.length as gff_attr_size, 'dsDNA' as gff_attr_molecule_type, --TODO add this back --SUBSTR(tn.name, 1, regexp_instr(tn.name || ' ', ' ', 1, 2) - 1) as gff_attr_organism_name, @@ -352,17 +352,11 @@ WHEN s.name = 'apicoplast_chromosome' THEN 'plastid' ELSE 'nuclear' END) as gff_attr_localization FROM webready.GenomicSeqAttributes_p gs, - dots.NaSequence ns, - sres.externaldatabase ed, - sres.externaldatabaserelease edr, sres.TaxonName tn, sres.Taxon t, sres.GeneticCode g, sres.OntologyTerm s - WHERE ns.na_sequence_id = gs.na_sequence_id - AND ns.external_database_release_id = edr.external_database_release_id - AND edr.external_database_id = ed.external_database_id - AND ns.taxon_id = tn.taxon_id + WHERE gs.taxon_id = tn.taxon_id AND tn.name_class = 'scientific name' AND gs.taxon_id = t.taxon_id AND gs.so_id = s.source_id From a44fa1ba4f5f985e462c9d9009edb1aeed0fae55 Mon Sep 17 00:00:00 2001 From: Steve <43149795+steve-fischer-200@users.noreply.github.com> Date: Tue, 9 Dec 2025 18:35:48 -0500 Subject: [PATCH 04/66] use partition keys for taxonspecies_p (#124) --- Model/lib/wdk/model/records/geneTableQueries.xml | 7 +++++++ Model/lib/wdk/model/records/transcriptAttributeQueries.xml | 1 + 2 files changed, 8 insertions(+) diff --git a/Model/lib/wdk/model/records/geneTableQueries.xml b/Model/lib/wdk/model/records/geneTableQueries.xml index bfb7ab9ac..628540bd5 100644 --- a/Model/lib/wdk/model/records/geneTableQueries.xml +++ b/Model/lib/wdk/model/records/geneTableQueries.xml @@ -164,6 +164,7 @@ AND ts.SPECIES_TAXON_ID = t.taxon_id AND ss.ncbi_tax_id = t.ncbi_tax_id and ga.org_abbrev IN (%%PARTITION_KEYS%%) + and ts.org_abbrev IN (%%PARTITION_KEYS%%) ) SELECT ta.gene_source_id AS source_id , ta.project_id @@ -512,6 +513,7 @@ AND ga.genus_species = sn.name AND dds.category in ('RNASeq','DNA Microarray Assay', 'SAGE', 'RT PCR') AND ga.org_abbrev IN (%%PARTITION_KEYS%%) + AND ts.org_abbrev IN (%%PARTITION_KEYS%%) GROUP BY ga.source_id, ga.project_id, ga.organism, ga.genus_species, graph_descrip.dataset, tn.name, dp.dataset_presenter_id, module,x_axis,y_axis, is_graph_custom,order_num, dds.category,dp.short_attribution --,ga.paralog_number @@ -623,6 +625,7 @@ AND ga.genus_species = sn.name AND dds.category = 'Protein expression (quantitative)' AND ga.org_abbrev IN (%%PARTITION_KEYS%%) + AND ts.org_abbrev IN (%%PARTITION_KEYS%%) ) g ]]> @@ -726,6 +729,7 @@ AND dds.name NOT LIKE '%CDS%' -- TODO: this is here for the horn dataset AND ga.genus_species = sn.name AND ga.org_abbrev IN (%%PARTITION_KEYS%%) + AND ts.org_abbrev IN (%%PARTITION_KEYS%%) ) g ]]> @@ -937,6 +941,7 @@ AND ga.genus_species = sn.name AND dds.category = 'Immunology' AND ga.org_abbrev IN (%%PARTITION_KEYS%%) + AND ts.org_abbrev IN (%%PARTITION_KEYS%%) ) g ) h , apidbtuning.datasetpresenter datapres @@ -1158,6 +1163,7 @@ from ( AND ga.genus_species = sn.name AND dds.category = 'Phenotype' AND ga.org_abbrev IN (%%PARTITION_KEYS%%) + AND ts.org_abbrev IN (%%PARTITION_KEYS%%) ) g ]]> @@ -1698,6 +1704,7 @@ from ( AND ga.genus_species = sn.name AND dds.category = 'Phenotype' AND ga.org_abbrev IN (%%PARTITION_KEYS%%) + AND ts.org_abbrev IN (%%PARTITION_KEYS%%) ) g ]]> diff --git a/Model/lib/wdk/model/records/transcriptAttributeQueries.xml b/Model/lib/wdk/model/records/transcriptAttributeQueries.xml index 0e4a97192..4c70ff4ef 100644 --- a/Model/lib/wdk/model/records/transcriptAttributeQueries.xml +++ b/Model/lib/wdk/model/records/transcriptAttributeQueries.xml @@ -1077,6 +1077,7 @@ ELSE 'N/A' end as apollo_link_out ) AND ds.taxon_id = ts.taxon_id AND ts.species_taxon_id = tn.taxon_id + AND ts.org_abbrev in (%%PARTITION_KEYS%%) ) d RIGHT JOIN webready.GeneAttributes_p ga ON ga.species = d.species WHERE ga.org_abbrev in (%%PARTITION_KEYS%%) ]]> From 624fc6854969ee80516391cdbdbb3514b294c022 Mon Sep 17 00:00:00 2001 From: John Brestelli Date: Tue, 9 Dec 2025 23:02:25 -0500 Subject: [PATCH 05/66] add get only syntenic orthologs (inner join) and add union for unity mapping reference --- .../LoadRefSynOrthologousGenesTable.psql | 40 ++++++++++--------- 1 file changed, 22 insertions(+), 18 deletions(-) diff --git a/Model/lib/psql/webready/comparative/LoadRefSynOrthologousGenesTable.psql b/Model/lib/psql/webready/comparative/LoadRefSynOrthologousGenesTable.psql index 093145e3a..3747f51cb 100644 --- a/Model/lib/psql/webready/comparative/LoadRefSynOrthologousGenesTable.psql +++ b/Model/lib/psql/webready/comparative/LoadRefSynOrthologousGenesTable.psql @@ -11,31 +11,35 @@ DECLARE BEGIN FOR orgrecord IN SELECT org_abbrev, sanitized_org_abbrev, ref_strain_abbrev as ref_org_abbrev - FROM :SCHEMA.organismabbreviation_p oa, apidb.organism o - WHERE oa.org_abbrev = o.abbrev + FROM :SCHEMA.organismabbreviation_p oa, apidb.organism o + WHERE oa.org_abbrev = o.abbrev LOOP INSERT INTO :SCHEMA.RefSynOrthologousGenes_p (source_id, ref_source_id, org_abbrev, project_id, modification_date) WITH syn_pairs AS ( - SELECT DISTINCT ga.source_id, sg.syn_na_feature_id as ref_na_feature_id - FROM :SCHEMA.SyntenicGene_p sg, :SCHEMA.GeneAttributes_p ga - WHERE sg.na_sequence_id = ga.na_sequence_id - AND ga.org_abbrev = orgrecord.org_abbrev - and sg.syn_organism_abbrev = orgrecord.ref_org_abbrev - AND sg.end_max >= ga.start_min - AND sg.start_min <= ga.end_max - ), + SELECT DISTINCT ga.source_id, sg.syn_na_feature_id as ref_na_feature_id + FROM :SCHEMA.SyntenicGene_p sg, :SCHEMA.GeneAttributes_p ga + WHERE sg.na_sequence_id = ga.na_sequence_id + AND ga.org_abbrev = orgrecord.org_abbrev + and sg.syn_organism_abbrev = orgrecord.ref_org_abbrev + AND sg.end_max >= ga.start_min + AND sg.start_min <= ga.end_max + ), ortholog_pairs AS (SELECT gog.gene_id as source_id, ga_ref.na_feature_id as ref_na_feature_id, gog_ref.gene_id as ref_source_id - FROM :SCHEMA.GeneOrthologGroup gog - JOIN :SCHEMA.GeneOrthologGroup gog_ref ON gog.group_id = gog_ref.group_id - JOIN :SCHEMA.GeneAttributes_p ga_ref on gog_ref.gene_id = ga_ref.source_id - WHERE gog.org_abbrev = orgrecord.org_abbrev - AND gog_ref.org_abbrev = orgrecord.ref_org_abbrev - and ga_ref.org_abbrev = orgrecord.ref_org_abbrev + FROM :SCHEMA.GeneOrthologGroup gog + JOIN :SCHEMA.GeneOrthologGroup gog_ref ON gog.group_id = gog_ref.group_id + JOIN :SCHEMA.GeneAttributes_p ga_ref on gog_ref.gene_id = ga_ref.source_id + WHERE gog.org_abbrev = orgrecord.org_abbrev + AND gog_ref.org_abbrev = orgrecord.ref_org_abbrev + and ga_ref.org_abbrev = orgrecord.ref_org_abbrev ) SELECT ortholog_pairs.source_id, ortholog_pairs.ref_source_id, orgrecord.org_abbrev, ':PROJECT_ID', current_timestamp FROM ortholog_pairs - LEFT JOIN syn_pairs ON ortholog_pairs.source_id = syn_pairs.source_id AND ortholog_pairs.ref_na_feature_id = syn_pairs.ref_na_feature_id:PLPGSQL_DELIM - + INNER JOIN syn_pairs ON ortholog_pairs.source_id = syn_pairs.source_id AND ortholog_pairs.ref_na_feature_id = syn_pairs.ref_na_feature_id + UNION + SELECT ga.source_id, ga.source_id as ref_source_id, ga.org_abbrev, ga.project_id, current_timestamp + FROM :SCHEMA.geneattributes_p ga + WHERE ga.org_abbrev = orgrecord.org_abbrev + AND ga.org_abbrev = orgrecord.ref_org_abbrev:PLPGSQL_DELIM END LOOP:PLPGSQL_DELIM END $$; From 4a56b4f444ab80bc064b0006ce0a79a293154734 Mon Sep 17 00:00:00 2001 From: John Brestelli Date: Tue, 9 Dec 2025 23:08:48 -0500 Subject: [PATCH 06/66] filter metatable by taxa --- Model/lib/wdk/model/records/geneTableQueries.xml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Model/lib/wdk/model/records/geneTableQueries.xml b/Model/lib/wdk/model/records/geneTableQueries.xml index 628540bd5..976693f1e 100644 --- a/Model/lib/wdk/model/records/geneTableQueries.xml +++ b/Model/lib/wdk/model/records/geneTableQueries.xml @@ -4200,7 +4200,7 @@ where org_abbrev in (%%PARTITION_KEYS%%) , ta.name AS organisms FROM ( - SELECT DISTINCT dmr.target_name, dmr.target_type, tn.name + SELECT DISTINCT dmr.target_name, dmr.target_type, tn.name, dd.taxon_id FROM ApidbTuning.DatasetDatasource dd INNER JOIN ApidbTuning.DatasetModelRef dmr ON dd.dataset_presenter_id = dmr.dataset_presenter_id @@ -4212,6 +4212,7 @@ where org_abbrev in (%%PARTITION_KEYS%%) , webready.GeneAttributes_p ga -- GROUP BY ga.source_id, ga.project_id, target_name, target_type WHERE ga.org_abbrev IN (%%PARTITION_KEYS%%) + AND ga.taxon_id = ta.taxon_id ORDER BY ga.source_id, target_name ]]> From baca6e50bd4d176ecf25d52375cb86104d54e05c Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Wed, 10 Dec 2025 13:30:39 -0500 Subject: [PATCH 07/66] adjust MetaTable query --- Model/lib/wdk/model/records/geneTableQueries.xml | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/Model/lib/wdk/model/records/geneTableQueries.xml b/Model/lib/wdk/model/records/geneTableQueries.xml index 976693f1e..050136490 100644 --- a/Model/lib/wdk/model/records/geneTableQueries.xml +++ b/Model/lib/wdk/model/records/geneTableQueries.xml @@ -4192,7 +4192,7 @@ where org_abbrev in (%%PARTITION_KEYS%%) + ]]> From a5ff61a799e0a259ae1c8155588988ceb86ab0f0 Mon Sep 17 00:00:00 2001 From: bindu Date: Wed, 10 Dec 2025 13:48:10 -0500 Subject: [PATCH 08/66] TODO : add cellularLocalizationWdkAttributes attr in attributeList, for cellularLocalizationEdaQuestion --- Model/lib/dst/cellularLocalization.dst | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Model/lib/dst/cellularLocalization.dst b/Model/lib/dst/cellularLocalization.dst index 72c83dfbf..f4be53f29 100644 --- a/Model/lib/dst/cellularLocalization.dst +++ b/Model/lib/dst/cellularLocalization.dst @@ -18,8 +18,9 @@ prop=cellularLocalizationWdkAttributes + Date: Wed, 10 Dec 2025 14:43:55 -0500 Subject: [PATCH 09/66] first pass at replace study and studylink with claude --- Model/lib/dst/expression.dst | 13 +- Model/lib/dst/quantProteomics.dst | 10 +- .../wdk/model/questions/params/geneParams.xml | 73 ++++++------ .../questions/queries/compoundQueries.xml | 12 +- .../model/questions/queries/geneQueries.xml | 62 +++++----- .../wdk/model/records/geneTableQueries.xml | 111 ++++++++---------- 6 files changed, 132 insertions(+), 149 deletions(-) diff --git a/Model/lib/dst/expression.dst b/Model/lib/dst/expression.dst index e09ed2434..df08174b2 100644 --- a/Model/lib/dst/expression.dst +++ b/Model/lib/dst/expression.dst @@ -19,21 +19,20 @@ from study.study s where name = '${datasetName}' /** -select distinct s.study_id as internal +select distinct s.node_set_id as internal , s.name as term - , REGEXP_REPLACE (s.name, '\[(.)+\]', '') AS display + , REGEXP_REPLACE (s.name, '\[(.)+\]', '') AS display , d.name -from study.study s - , study.studylink sl +from study.nodeset s + , study.nodenodeset sl , RESULTS.NAFEATUREDIFFRESULT dr , SRES.EXTERNALDATABASERELEASE r , sres.externaldatabase d -where +where s.EXTERNAL_DATABASE_RELEASE_ID = r.EXTERNAL_DATABASE_RELEASE_ID and r.EXTERNAL_DATABASE_ID = d.EXTERNAL_DATABASE_ID -and s.study_id = sl.study_id +and s.node_set_id = sl.node_set_id and sl.PROTOCOL_APP_NODE_ID = dr.PROTOCOL_APP_NODE_ID -and s.INVESTIGATION_ID is null and d.name = '${datasetName}' ORDER BY s.name desc **/ diff --git a/Model/lib/dst/quantProteomics.dst b/Model/lib/dst/quantProteomics.dst index 15ffc2319..d7b321dee 100644 --- a/Model/lib/dst/quantProteomics.dst +++ b/Model/lib/dst/quantProteomics.dst @@ -83,17 +83,17 @@ prop=dataType -select distinct s.study_id as internal, s.name as term, s.name as display -from study.study s, sres.externaldatabase ed, sres.externaldatabaserelease edr - ,results.nafeaturediffresult ndr, study.protocolappnode pan, study.studylink sl +select distinct s.node_set_id as internal, s.name as term, s.name as display +from study.nodeset s, sres.externaldatabase ed, sres.externaldatabaserelease edr + ,results.nafeaturediffresult ndr, study.protocolappnode pan, study.nodenodeset sl where ed.external_database_id=edr.external_database_id and s.external_database_release_id = edr.external_database_release_id and ed.name='${datasetName}' -and s.study_id = sl.study_id +and s.node_set_id = sl.node_set_id and sl.protocol_app_node_id = pan.protocol_app_node_id and ndr.protocol_app_node_id = pan.protocol_app_node_id and s.name NOT like 'Quantitative Mass Spec%' -order by s.study_id +order by s.node_set_id diff --git a/Model/lib/wdk/model/questions/params/geneParams.xml b/Model/lib/wdk/model/questions/params/geneParams.xml index 73d557f1c..a8d8c744c 100644 --- a/Model/lib/wdk/model/questions/params/geneParams.xml +++ b/Model/lib/wdk/model/questions/params/geneParams.xml @@ -6558,9 +6558,8 @@ products of your selected type (or types).

WHEN s.name ='BSF Const MetaCycle' THEN 'BSF Const' WHEN s.name ='PF Alt MetaCycle' THEN 'PF Alt' ELSE 'PF Const' END AS term - FROM study.study s, study.study i - WHERE i.name = 'tbruTREU927_Rijo_Circadian_Regulation_ebi_rnaSeq_RSRC' - AND i.study_id = s.INVESTIGATION_ID and s.name like '%MetaCycle%' + FROM study.nodeset s + WHERE s.name like '%MetaCycle%' @@ -6616,10 +6615,10 @@ products of your selected type (or types).

FROM sres.externaldatabase d , sres.externaldatabaserelease r , apidb.nafeatureWGCNAResults fwr - , study.studylink sl - , study.study s + , study.nodenodeset sl + , study.nodeset s WHERE sl.protocol_app_node_id = fwr.protocol_app_node_id - AND sl.study_id= s.study_id + AND sl.node_set_id= s.node_set_id AND r.external_database_release_id = s.external_database_release_id AND d.external_database_id = r.external_database_id ]]> @@ -6643,10 +6642,10 @@ products of your selected type (or types).

pan.protocol_app_node_id as internal , regexp_replace(pan.name,'(((\w+)\s){1}).*', '\1') as display --clean pan.name by keeping only the first full word from study.protocolappnode pan - , study.study s - , study.studylink sl + , study.nodeset s + , study.nodenodeset sl where s.external_database_release_id = $$wgcnaDataset$$ - and s.study_id = sl.study_id + and s.node_set_id = sl.node_set_id and sl.protocol_app_node_id = pan.protocol_app_node_id and pan.name like '%module%' ) a @@ -6669,10 +6668,10 @@ products of your selected type (or types).

FROM sres.externaldatabase d , sres.externaldatabaserelease r , apidb.nafeaturelist fl - , study.studylink sl - , study.study s + , study.nodenodeset sl + , study.nodeset s WHERE sl.protocol_app_node_id = fl.protocol_app_node_id - AND sl.study_id= s.study_id + AND sl.node_set_id= s.node_set_id AND r.external_database_release_id = s.external_database_release_id AND d.external_database_id = r.external_database_id ]]> @@ -6688,9 +6687,9 @@ products of your selected type (or types).

@@ -6757,9 +6756,9 @@ products of your selected type (or types).

CASE WHEN pan.name ='outlier (lopit)' THEN CONCAT('- ', upper(substr(CONCAT(replace(pan.name,' (lopit)',''), ' probability'),1,1)), substr(CONCAT(replace(pan.name,' (lopit)',''), ' probability'),2,9999)) ELSE CONCAT(upper(substr(CONCAT(replace(pan.name,' (lopit)',''), ' probability'),1,1)), substr(CONCAT(replace(pan.name,' (lopit)',''), ' probability'),2,9999)) END as display_name , cast(null as varchar(1)) as description, cast(null as varchar(1)) as units, 'number' as type,1 as is_range,1 as precision, cast(null as varchar(1)) as display_order - FROM study.study s , study.studyLink sl, study.ProtocolAppNode pan, apidb.LopitResults lr, apidbtuning.GeneAttributes ga + FROM study.nodeset s , study.nodenodeset sl, study.ProtocolAppNode pan, apidb.LopitResults lr, apidbtuning.GeneAttributes ga WHERE s.name = $$lopit_method$$ - AND s.study_id = sl.study_id + AND s.node_set_id = sl.node_set_id AND sl.protocol_app_node_id = pan.protocol_app_node_id AND pan.protocol_app_node_id = lr.protocol_app_node_id AND ga.na_feature_id = lr.na_feature_id @@ -6778,17 +6777,17 @@ products of your selected type (or types).


, d.name as internal FROM sres.externaldatabase d , sres.externaldatabaserelease r - , study.study s - , study.studylink sl + , study.nodeset s + , study.nodenodeset sl , apidb.phenotypescore ps WHERE d.external_database_id = r.external_database_id AND r.external_database_release_id = s.external_database_release_id - AND s.study_id = sl.study_id + AND s.node_set_id = sl.node_set_id AND sl.protocol_app_node_id = ps.protocol_app_node_id ]]> @@ -7027,14 +7026,14 @@ products of your selected type (or types).

FROM apidb.PhenotypeScore ps , study.protocolappnode pan , (SELECT DISTINCT sl.protocol_app_node_id, d.name - FROM study.study s - , study.studylink sl + FROM study.nodeset s + , study.nodenodeset sl , sres.externaldatabase d , sres.externaldatabaserelease r WHERE d.name = '$$phenotypeScoreDataset$$' and d.external_database_id = r.external_database_id and r.external_database_release_id = s.external_database_release_id - and s.study_id = sl.study_id + and s.node_set_id = sl.node_set_id ) sl WHERE ps.protocol_app_node_id = pan.protocol_app_node_id AND pan.protocol_app_node_id = sl.protocol_app_node_id @@ -7070,14 +7069,14 @@ products of your selected type (or types).

, study.protocolappnode pan , ( SELECT distinct sl.protocol_app_node_id, d.name - FROM study.study s - , study.studylink sl + FROM study.nodeset s + , study.nodenodeset sl , sres.externaldatabase d , sres.externaldatabaserelease r WHERE d.name = '$$phenotypeScoreDataset$$' AND d.external_database_id = r.external_database_id AND r.external_database_release_id = s.external_database_release_id - AND s.study_id = sl.study_id + AND s.node_set_id = sl.node_set_id ) sl WHERE p.protocol_app_node_id = pan.protocol_app_node_id and pan.protocol_app_node_id = sl.protocol_app_node_id @@ -7159,9 +7158,9 @@ products of your selected type (or types).

, null::numeric as number_value , lower(p.value) as string_value , cast(null as timestamp) as date_value - FROM apidb.nafeaturephenotype p, study.study s, study.studylink sl + FROM apidb.nafeaturephenotype p, study.nodeset s, study.nodenodeset sl WHERE s.name = 'ncraOR74A_phenotype_GeneImage_NAFeaturePhenotypeImage_RSRC' - AND s.study_id = sl.study_id + AND s.node_set_id = sl.node_set_id AND sl.protocol_app_node_id = p.protocol_app_node_id ]]> @@ -7187,9 +7186,9 @@ products of your selected type (or types).

, 'string' as type , 0 as is_range , 1 as precision - FROM apidb.nafeaturephenotype p, study.study s, study.studylink sl + FROM apidb.nafeaturephenotype p, study.nodeset s, study.nodenodeset sl WHERE s.name = 'ncraOR74A_phenotype_GeneImage_NAFeaturePhenotypeImage_RSRC' - AND s.study_id = sl.study_id + AND s.node_set_id = sl.node_set_id AND sl.protocol_app_node_id = p.protocol_app_node_id ORDER BY initcap(p.property) ]]> @@ -7210,9 +7209,9 @@ products of your selected type (or types).

, null::numeric as number_value , p.value as string_value , cast(null as timestamp) as date_value - FROM apidb.nafeaturephenotype p, study.study s, study.studylink sl + FROM apidb.nafeaturephenotype p, study.nodeset s, study.nodenodeset sl WHERE s.name like '%_PHI-base_curated_phenotype_NAFeaturePhenotypeGeneric_RSRC' - AND s.study_id = sl.study_id + AND s.node_set_id = sl.node_set_id AND sl.protocol_app_node_id = p.protocol_app_node_id AND p.property NOT IN ('Co-mutated gene(s)','Gene inducer','PHI-base entry','PMID') AND p.property NOT like 'Comments%' @@ -7240,9 +7239,9 @@ products of your selected type (or types).

, 'string' as type , 0 as is_range , 1 as precision - FROM apidb.nafeaturephenotype p, study.study s, study.studylink sl + FROM apidb.nafeaturephenotype p, study.nodeset s, study.nodenodeset sl WHERE s.name like '%_PHI-base_curated_phenotype_NAFeaturePhenotypeGeneric_RSRC' - AND s.study_id = sl.study_id + AND s.node_set_id = sl.node_set_id AND sl.protocol_app_node_id = p.protocol_app_node_id AND p.property NOT IN ('Co-mutated gene(s)','Gene inducer','PHI-base entry','PMID') AND p.property NOT like 'Comments%' diff --git a/Model/lib/wdk/model/questions/queries/compoundQueries.xml b/Model/lib/wdk/model/questions/queries/compoundQueries.xml index 9083f4b03..1c457c017 100644 --- a/Model/lib/wdk/model/questions/queries/compoundQueries.xml +++ b/Model/lib/wdk/model/questions/queries/compoundQueries.xml @@ -660,12 +660,12 @@ SELECT SUM(r.value) AS value , r.compound_id FROM apidbtuning.profileType pt - , study.study s - , study.studyLink sl + , study.nodeset s + , study.nodenodeset sl , study.protocolAppNode pan , results.compoundMassSpec r WHERE pt.profile_set_name = s.name - AND sl.study_id = s.study_id + AND sl.node_set_id = s.node_set_id AND sl.protocol_app_node_id = pan.protocol_app_node_id AND pan.protocol_app_node_id = r.protocol_app_node_id AND pan.protocol_app_node_id in ($$samples_fc_ref_generic$$) @@ -684,12 +684,12 @@ SELECT SUM(r.value) AS value , r.compound_id FROM apidbtuning.profileType pt - , study.study s - , study.studyLink sl + , study.nodeset s + , study.nodenodeset sl , study.protocolAppNode pan , results.compoundMassSpec r WHERE pt.profile_set_name = s.name - AND sl.study_id = s.study_id + AND sl.node_set_id = s.node_set_id AND sl.protocol_app_node_id = pan.protocol_app_node_id AND pan.protocol_app_node_id = r.protocol_app_node_id AND pan.protocol_app_node_id in ($$samples_fc_comp_generic$$) diff --git a/Model/lib/wdk/model/questions/queries/geneQueries.xml b/Model/lib/wdk/model/questions/queries/geneQueries.xml index d762b635c..01dca4a43 100644 --- a/Model/lib/wdk/model/questions/queries/geneQueries.xml +++ b/Model/lib/wdk/model/questions/queries/geneQueries.xml @@ -205,9 +205,9 @@ concat('$$metacycle_protocol$$', '%') , ( SELECT DISTINCT regexp_replace(s.name, '[[:space:]]{1,}', '_') AS term - FROM study.study s, study.studyLink sl + FROM study.nodeset s, study.nodenodeset sl WHERE s.name = '$$metacycle_study_generic$$' - AND s.investigation_id = sl.study_id + AND s.node_set_id = sl.node_set_id ) ) , '%' @@ -227,9 +227,9 @@ SELECT DISTINCT protocol_app_node_id FROM ( SELECT sl.* - FROM study.study s, study.studyLink sl + FROM study.nodeset s, study.nodenodeset sl WHERE s.name = '$$metacycle_study_generic$$' - AND s.investigation_id = sl.study_id + AND s.node_set_id = sl.node_set_id ) t ) AND t.GENE_NA_FEATURE_ID = mc.NA_FEATURE_ID @@ -242,9 +242,9 @@ concat('ARSresult_', '%') , ( SELECT DISTINCT regexp_replace(s.name, '[[:space:]]{1,}', '_') AS term - FROM study.study s, study.studyLink sl + FROM study.nodeset s, study.nodenodeset sl WHERE s.name = '$$metacycle_study_generic$$' - AND s.investigation_id = sl.study_id + AND s.node_set_id = sl.node_set_id ) ) , '%' @@ -270,9 +270,9 @@ concat('JTKresult_', '%') , ( SELECT DISTINCT regexp_replace(s.name, '[[:space:]]{1,}', '_') AS term - FROM study.study s, study.studyLink sl + FROM study.nodeset s, study.nodenodeset sl WHERE s.name = '$$metacycle_study_generic$$' - AND s.investigation_id = sl.study_id + AND s.node_set_id = sl.node_set_id ) ) , '%') @@ -282,9 +282,9 @@ SELECT DISTINCT protocol_app_node_id FROM ( SELECT sl.* - FROM study.study s, study.studyLink sl + FROM study.nodeset s, study.nodenodeset sl WHERE s.name = '$$metacycle_study_generic$$' - AND s.investigation_id = sl.study_id + AND s.node_set_id = sl.node_set_id ) t ) AND t.GENE_NA_FEATURE_ID = mc.NA_FEATURE_ID @@ -300,9 +300,9 @@ WHERE name LIKE concat(concat(concat('$$metacycle_protocol$$', '%'), ( SELECT DISTINCT regexp_replace(s.name, '[[:space:]]{1,}', '_') AS term - FROM study.study s, study.studyLink sl + FROM study.nodeset s, study.nodenodeset sl WHERE s.name = '$$metacycle_study_generic$$' - AND s.investigation_id = sl.study_id + AND s.node_set_id = sl.node_set_id )), '%') ) SELECT t.source_id @@ -319,9 +319,9 @@ SELECT DISTINCT protocol_app_node_id FROM ( SELECT sl.* - FROM study.study s, study.studyLink sl + FROM study.nodeset s, study.nodenodeset sl WHERE s.name = '$$metacycle_study_generic$$' - AND s.investigation_id = sl.study_id + AND s.node_set_id = sl.node_set_id ) t ) AND t.GENE_NA_FEATURE_ID = mc.NA_FEATURE_ID @@ -332,9 +332,9 @@ AND pan.name LIKE concat(concat(concat('JTKresult_', '%'), ( SELECT DISTINCT regexp_replace(s.name, '[[:space:]]{1,}', '_') AS term - FROM study.study s, study.studyLink sl + FROM study.nodeset s, study.nodenodeset sl WHERE s.name = '$$metacycle_study_generic$$' - AND s.investigation_id = sl.study_id + AND s.node_set_id = sl.node_set_id )), '%') ) table3 , ( @@ -356,9 +356,9 @@ WHERE name LIKE concat(concat(concat('ARSresult_', '%'), ( SELECT DISTINCT regexp_replace(s.name, '[[:space:]]{1,}', '_') AS term - FROM study.study s, study.studyLink sl + FROM study.nodeset s, study.nodenodeset sl WHERE s.name = '$$metacycle_study_generic$$' - AND s.investigation_id = sl.study_id + AND s.node_set_id = sl.node_set_id )), '%') ) t ) @@ -367,9 +367,9 @@ FROM ( SELECT sl.* - FROM study.study s, study.studyLink sl + FROM study.nodeset s, study.nodenodeset sl WHERE s.name = '$$metacycle_study_generic$$' - AND s.investigation_id = sl.study_id + AND s.node_set_id = sl.node_set_id ) t ) AND t.GENE_NA_FEATURE_ID = mc.NA_FEATURE_ID @@ -400,9 +400,9 @@ with genePick as ( select ta.gene_source_id, pan.name - from study.study s , study.studyLink sl, study.ProtocolAppNode pan, apidb.WGCNAResults res, webready.TranscriptAttributes_p ta + from study.nodeset s , study.nodenodeset sl, study.ProtocolAppNode pan, apidb.WGCNAResults res, webready.TranscriptAttributes_p ta where s.name = 'iterativeWGCNA Dual transcriptomes of malaria-infected Gambian children' - and s.study_id = sl.study_id + and s.node_set_id = sl.node_set_id and sl.protocol_app_node_id = pan.protocol_app_node_id and pan.protocol_app_node_id = res.protocol_app_node_id and ta.gene_na_feature_id = res.na_feature_id @@ -410,9 +410,9 @@ ) select ta.source_id, ta.gene_source_id, ta.project_id, REPLACE(pan.name,' (wgcna)','') as module_name, res.correlation_coefficient as kME, 'Y' as matched_result - from study.study s , study.studyLink sl, study.ProtocolAppNode pan, apidb.WGCNAResults res, webready.TranscriptAttributes_p ta, genePick + from study.nodeset s , study.nodenodeset sl, study.ProtocolAppNode pan, apidb.WGCNAResults res, webready.TranscriptAttributes_p ta, genePick where s.name = 'iterativeWGCNA Dual transcriptomes of malaria-infected Gambian children' - and s.study_id = sl.study_id + and s.node_set_id = sl.node_set_id and sl.protocol_app_node_id = pan.protocol_app_node_id and pan.protocol_app_node_id = res.protocol_app_node_id and ta.gene_na_feature_id = res.na_feature_id @@ -3465,13 +3465,13 @@ study.protocolappparam ap, study.protocolparam p, study.output i, - study.studylink sl, + study.nodenodeset sl, STUDY.PROTOCOLAPPNODE an WHERE an.name LIKE '%DESeq%' AND p.protocol_param_id = ap.protocol_param_id AND ap.protocol_app_id = i.protocol_app_id AND i.PROTOCOL_APP_NODE_ID = an.PROTOCOL_APP_NODE_ID - AND sl.study_id = $$profileset_generic$$ + AND sl.node_set_id = $$profileset_generic$$ AND i.protocol_app_node_id = sl.protocol_app_node_id AND ((p.name = 'reference' AND ap.value = $$samples_de_ref_generic_deseq$$) OR (ap.value = $$samples_de_comp_generic_deseq$$ AND p.name = 'comparator')) @@ -5486,17 +5486,15 @@ select distinct ta.gene_source_id FROM results.nafeatureexpression nfe , webready.TranscriptAttributes_p ta , study.protocolappnode pan - , study.studylink sl - , study.study ps - , study.study i + , study.nodenodeset sl + , study.nodeset ps , sres.externaldatabaserelease r , sres.externaldatabase d WHERE ta.gene_na_feature_id = nfe.na_feature_id AND nfe.protocol_app_node_id = pan.protocol_app_node_id AND pan.protocol_app_node_id = sl.protocol_app_node_id - AND sl.study_id = ps.study_id - AND ps.investigation_id = i.study_id - AND i.external_database_release_id = r.external_database_release_id + AND sl.node_set_id = ps.node_set_id + AND ps.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 nfe.VALUE >= $$min_glycosome_score$$ diff --git a/Model/lib/wdk/model/records/geneTableQueries.xml b/Model/lib/wdk/model/records/geneTableQueries.xml index 050136490..abaaee24d 100644 --- a/Model/lib/wdk/model/records/geneTableQueries.xml +++ b/Model/lib/wdk/model/records/geneTableQueries.xml @@ -84,12 +84,12 @@ , ed.DATASET_PRESENTER_DISPLAY_NAME from apidb.nafeaturelist fl , webready.GeneAttributes_p ga - , study.studylink sl + , study.nodenodeset sl , study.protocolappnode pan - , study.study s + , study.nodeset s , APIDBTUNING.EXTERNALDBDATASETPRESENTER ed where sl.protocol_app_node_id = fl.protocol_app_node_id - and sl.study_id= s.study_id + and sl.node_set_id= s.node_set_id and fl.na_feature_id = ga.na_feature_id and sl.PROTOCOL_APP_NODE_ID = pan.PROTOCOL_APP_NODE_ID and s.EXTERNAL_DATABASE_RELEASE_ID = ed.EXTERNAL_DATABASE_RELEASE_ID @@ -117,12 +117,12 @@ , ed.DATASET_PRESENTER_DISPLAY_NAME from apidb.nafeaturelist fl , webready.GeneAttributes_p ga - , study.studylink sl + , study.nodenodeset sl , study.protocolappnode pan - , study.study s + , study.nodeset s , APIDBTUNING.EXTERNALDBDATASETPRESENTER ed where sl.protocol_app_node_id = fl.protocol_app_node_id - and sl.study_id= s.study_id + and sl.node_set_id= s.node_set_id and fl.na_feature_id = ga.na_feature_id and sl.PROTOCOL_APP_NODE_ID = pan.PROTOCOL_APP_NODE_ID and s.EXTERNAL_DATABASE_RELEASE_ID = ed.EXTERNAL_DATABASE_RELEASE_ID @@ -1371,9 +1371,9 @@ from ( , CASE WHEN property = 'Tissue' THEN value END AS tissue , CASE WHEN property = 'Vegetative spores' THEN value END AS vegetativespores FROM APIDB.NAFEATUREPHENOTYPE r, webready.GeneAttributes_p ga, - study.protocolappnode pan, study.study s, study.studylink sl + study.protocolappnode pan, study.nodeset s, study.nodenodeset sl WHERE pan.PROTOCOL_APP_NODE_ID = r.PROTOCOL_APP_NODE_ID - and s.study_id = sl.study_id + and s.node_set_id = sl.node_set_id and sl.protocol_app_node_id = pan.protocol_app_node_id and s.name LIKE '%PHI-base_curated_phenotype_NAFeaturePhenotypeGeneric_RSRC' AND r.NA_FEATURE_ID = ga.NA_FEATURE_ID @@ -1451,9 +1451,9 @@ from ( , CASE WHEN property = 'Virulence Model' THEN value AS virulencemodel , CASE WHEN property = 'Species' THEN value AS species from apidb.nafeaturephenotype r, webready.GeneAttributes_p ga, - study.protocolappnode pan, study.study s , study.studyLink sl + study.protocolappnode pan, study.nodeset s , study.nodenodeset sl where pan.protocol_app_node_id = r.protocol_app_node_id - and s.study_id = sl.study_id + and s.node_set_id = sl.node_set_id and sl.protocol_app_node_id = pan.protocol_app_node_id and s.name LIKE '%_CGD_pheno_NAFeaturePhenotypeGeneric_RSRC' and r.na_feature_id = ga.na_feature_id @@ -2417,9 +2417,9 @@ from ( Date: Wed, 10 Dec 2025 15:35:33 -0500 Subject: [PATCH 10/66] fix TFBSGene_p.psql --- Model/lib/psql/webready/orgSpecific/TFBSGene_p.psql | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/Model/lib/psql/webready/orgSpecific/TFBSGene_p.psql b/Model/lib/psql/webready/orgSpecific/TFBSGene_p.psql index 6985b6d7b..555d40fa3 100644 --- a/Model/lib/psql/webready/orgSpecific/TFBSGene_p.psql +++ b/Model/lib/psql/webready/orgSpecific/TFBSGene_p.psql @@ -32,7 +32,9 @@ ELSE '+' END END as direction - -- , aef.* + , aef.primary_score + , aef.name + , aef.external_database_release_id FROM dots.BindingSiteFeature aef, apidb.FeatureLocation arrloc, :SCHEMA.GeneAttributes_p ga From 4bddc854f3a437fe8273f44a2589d3dfe8ed3342 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Wed, 10 Dec 2025 18:58:22 -0500 Subject: [PATCH 11/66] add maxRecommended msg to org params --- .../model/questions/params/organismParams.xml | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) diff --git a/Model/lib/wdk/model/questions/params/organismParams.xml b/Model/lib/wdk/model/questions/params/organismParams.xml index 7de643449..8bf999fcc 100644 --- a/Model/lib/wdk/model/questions/params/organismParams.xml +++ b/Model/lib/wdk/model/questions/params/organismParams.xml @@ -1,5 +1,9 @@ + 5 + You have selected more than five organisms. This will lead to slow responses. If you can, please select fewer. Also, be sure to set your Organism Preferences for an enhanced site experience + + @@ -55,6 +59,12 @@ showOnlyPreferredOrganisms highlightReferenceOrganisms + + "%%maxRecommendedOrganisms%%" + + + "%%maxRecommendedMessage%%" + @@ -76,6 +86,12 @@ showOnlyPreferredOrganisms highlightReferenceOrganisms + + "%%maxRecommendedOrganisms%%" + + + "%%maxRecommendedMessage%%" + @@ -99,6 +115,12 @@ showOnlyPreferredOrganisms highlightReferenceOrganisms + + "%%maxRecommendedOrganisms%%" + + + "%%maxRecommendedMessage%%" + showOnlyPreferredOrganisms highlightReferenceOrganisms + + "%%maxRecommendedOrganisms%%" + + + "%%maxRecommendedMessage%%" + @@ -140,6 +168,12 @@ highlightReferenceOrganisms + + "%%maxRecommendedOrganisms%%" + + + "%%maxRecommendedMessage%%" + showOnlyPreferredOrganisms highlightReferenceOrganisms + + "%%maxRecommendedOrganisms%%" + + + "%%maxRecommendedMessage%%" + @@ -210,6 +250,12 @@ showOnlyPreferredOrganisms highlightReferenceOrganisms + + "%%maxRecommendedOrganisms%%" + + + "%%maxRecommendedMessage%%" + + + "%%maxRecommendedOrganisms%%" + + + "%%maxRecommendedMessage%%" + @@ -236,6 +288,12 @@ showOnlyPreferredOrganisms highlightReferenceOrganisms + + "%%maxRecommendedOrganisms%%" + + + "%%maxRecommendedMessage%%" + Select the organism(s) you wish to query. + + "%%maxRecommendedOrganisms%%" + + + "%%maxRecommendedMessage%%" + Select the organism(s) you wish to query. + + "%%maxRecommendedOrganisms%%" + + + "%%maxRecommendedMessage%%" + @@ -291,6 +361,12 @@ showOnlyPreferredOrganisms + + "%%maxRecommendedOrganisms%%" + + + "%%maxRecommendedMessage%%" + Date: Wed, 10 Dec 2025 19:54:43 -0500 Subject: [PATCH 12/66] fix all remianing instances of study.studylink --- .../wdk/model/questions/params/geneParams.xml | 22 +++++++++---------- .../model/questions/params/popsetParams.xml | 4 ++-- .../model/questions/params/sharedParams.xml | 12 +++++----- .../model/questions/queries/popsetQueries.xml | 4 ++-- .../wdk/model/records/popsetTableQueries.xml | 6 ++--- .../wdk/model/records/sampleTableQueries.xml | 6 ++--- 6 files changed, 26 insertions(+), 28 deletions(-) diff --git a/Model/lib/wdk/model/questions/params/geneParams.xml b/Model/lib/wdk/model/questions/params/geneParams.xml index a8d8c744c..32b322762 100644 --- a/Model/lib/wdk/model/questions/params/geneParams.xml +++ b/Model/lib/wdk/model/questions/params/geneParams.xml @@ -8032,8 +8032,8 @@ products of your selected type (or types).

pan.protocol_app_node_id as internal, 'Uninduced sample' as display from study.protocolappnode pan - , study.studylink sl - where sl.study_id = $$profileset_generic$$ + , study.nodenodeset sl + where sl.node_set_id = $$profileset_generic$$ and sl.protocol_app_node_id = pan.protocol_app_node_id and pan.name like 'No_Tet%tpm%' @@ -8055,8 +8055,8 @@ products of your selected type (or types).

WHEN (pan.name like 'DIF%') THEN CONCAT('Induced throughout differentiation (DIF = 7 BS doublings + 6 PS doublings)', chr(185)) END as display FROM study.protocolappnode pan - , study.studylink sl - WHERE sl.study_id = $$profileset_generic$$ + , study.nodenodeset sl + WHERE sl.node_set_id = $$profileset_generic$$ AND sl.protocol_app_node_id = pan.protocol_app_node_id AND pan.name not like 'No_Tet%' AND pan.name like '%tpm%' @@ -9213,12 +9213,12 @@ end as term , pan.PROTOCOL_APP_NODE_ID as internal , pan2.name as display , pan2.node_order_num - FROM study.studylink sl + FROM study.nodenodeset sl , study.protocolappnode pan , RESULTS.NAFEATUREDIFFRESULT dr , webready.PANIO_p io , study.protocolappnode pan2 - WHERE sl.study_id = '$$profileset_generic$$' + WHERE sl.node_set_id = '$$profileset_generic$$' AND sl.PROTOCOL_APP_NODE_ID = pan.PROTOCOL_APP_NODE_ID AND pan.PROTOCOL_APP_NODE_ID = dr.PROTOCOL_APP_NODE_ID AND pan.protocol_app_node_id = io.output_pan_id @@ -9333,13 +9333,13 @@ end as term ) SELECT distinct ap.value as term, ap.value as internal, ap.value as display, ps.node_order_num FROM Study.ProtocolAppNode an, Study.ProtocolAppParam ap, - Study.StudyLink sl, Study.Study s, Study.Output o, perc_samples ps - WHERE sl.study_id = $$profileset_generic$$ + Study.nodenodeset sl, Study.nodeset s, Study.Output o, perc_samples ps + WHERE sl.node_set_id = $$profileset_generic$$ AND o.protocol_app_node_id = sl.protocol_app_node_id AND o.protocol_app_id = ap.protocol_app_id AND an.name like '%DESeq%' AND o.protocol_app_node_id = an.protocol_app_node_id - AND sl.study_id = s.study_id + AND sl.node_set_id = s.node_set_id AND ps.study_name = regexp_replace (s.name, ' \[.+\]', '') AND ap.value = ps.protocol_app_node_name ORDER BY ps.node_order_num @@ -9399,10 +9399,10 @@ end as term SELECT DISTINCT ndr.protocol_app_node_id as internal, pan.name as term, pan.name as display - FROM results.nafeaturediffresult ndr, study.protocolappnode pan, study.studylink sl + FROM results.nafeaturediffresult ndr, study.protocolappnode pan, study.nodenodeset sl WHERE pan.protocol_app_node_id = sl.protocol_app_node_id AND ndr.protocol_app_node_id = pan.protocol_app_node_id - AND sl.study_id = '$$profileset_generic$$' + AND sl.node_set_id = '$$profileset_generic$$' diff --git a/Model/lib/wdk/model/questions/params/popsetParams.xml b/Model/lib/wdk/model/questions/params/popsetParams.xml index b568e439e..3245b56ef 100644 --- a/Model/lib/wdk/model/questions/params/popsetParams.xml +++ b/Model/lib/wdk/model/questions/params/popsetParams.xml @@ -450,11 +450,11 @@ r.title as internal FROM SRES.BIBLIOGRAPHICREFERENCE r , study.studybibref sbr - , study.studylink sl + , study.nodenodeset sl , apidbtuning.popsetattributes pa WHERE r.title is not null AND r.bibliographic_reference_id = sbr.bibliographic_reference_id - AND sbr.study_id = sl.study_id + AND sbr.node_set_id = sl.node_set_id AND sl.protocol_app_node_id = pa.protocol_app_node_id ORDER BY r.title ]]> diff --git a/Model/lib/wdk/model/questions/params/sharedParams.xml b/Model/lib/wdk/model/questions/params/sharedParams.xml index 3b63f0d43..9978ebb0a 100644 --- a/Model/lib/wdk/model/questions/params/sharedParams.xml +++ b/Model/lib/wdk/model/questions/params/sharedParams.xml @@ -2886,21 +2886,19 @@ This parameter allows you to apply the minimum number of peptides to each select diff --git a/Model/lib/wdk/model/questions/queries/popsetQueries.xml b/Model/lib/wdk/model/questions/queries/popsetQueries.xml index 1d7c5e437..0ac93b5a1 100644 --- a/Model/lib/wdk/model/questions/queries/popsetQueries.xml +++ b/Model/lib/wdk/model/questions/queries/popsetQueries.xml @@ -144,11 +144,11 @@ from apidbtuning.PopsetAttributes s select pa.source_id, pa.project_id from SRES.BIBLIOGRAPHICREFERENCE br , study.studybibref sbr - , study.studylink sl + , study.nodenodeset sl , apidbtuning.popsetattributes pa where br.title = $$study$$ and br.BIBLIOGRAPHIC_REFERENCE_ID = sbr.BIBLIOGRAPHIC_REFERENCE_ID - and sbr.study_id = sl.study_id + and sbr.node_set_id = sl.node_set_id and sl.PROTOCOL_APP_NODE_ID = pa.PROTOCOL_APP_NODE_ID ]]> diff --git a/Model/lib/wdk/model/records/popsetTableQueries.xml b/Model/lib/wdk/model/records/popsetTableQueries.xml index 5f6ccc084..02bddd1e9 100644 --- a/Model/lib/wdk/model/records/popsetTableQueries.xml +++ b/Model/lib/wdk/model/records/popsetTableQueries.xml @@ -341,10 +341,10 @@ and bc.ontology_entry_id = oe.ontology_entry_id CASE WHEN title IS NULL then 'N/A' WHEN title = 'Direct Submission' then 'N/A' ELSE CONCAT('view') end AS studyLink - FROM ApidbTuning.PopsetAttributes ia, Study.StudyLink sl, - Study.StudyBibRef bib, sres.BibliographicReference ref + FROM ApidbTuning.PopsetAttributes ia, Study.nodenodeset sl, + Study.StudyBibRef bib, sres.BibliographicReference ref WHERE ia.protocol_app_node_id = sl.protocol_app_node_id - AND sl.study_id = bib.study_id + AND sl.node_set_id = bib.node_set_id AND bib.bibliographic_reference_id = ref.bibliographic_reference_id ]]> diff --git a/Model/lib/wdk/model/records/sampleTableQueries.xml b/Model/lib/wdk/model/records/sampleTableQueries.xml index f19b732e4..df9747986 100644 --- a/Model/lib/wdk/model/records/sampleTableQueries.xml +++ b/Model/lib/wdk/model/records/sampleTableQueries.xml @@ -80,12 +80,12 @@ , edp.dataset_presenter_id FROM apidbtuning.SampleProcess sd , apidbTuning.PanResults panr - , study.Study s - , study.StudyLink sl + , study.nodeset s + , study.nodenodeset sl , apidbTuning.ExternalDbDatasetPresenter edp WHERE sd.output_pan_id = panr.pan_id AND panr.pan_id = sl.protocol_app_node_id - AND sl.study_id = s.study_id + AND sl.node_set_id = s.node_set_id AND s.external_database_release_id = edp.external_database_release_id) q WHERE q.dataset_presenter_id = dsp.dataset_presenter_id ]]> From fce42ed31c3d1153b6bff7121642f87617225bdc Mon Sep 17 00:00:00 2001 From: John Brestelli Date: Wed, 10 Dec 2025 20:04:37 -0500 Subject: [PATCH 13/66] changed the remaining study.study and studylink to nodeset and nodenodeset --- .../model/questions/params/compoundParams.xml | 14 +++++------ .../wdk/model/questions/params/geneParams.xml | 24 ++++++++++--------- .../model/questions/params/organismParams.xml | 3 +-- .../wdk/model/records/geneTableQueries.xml | 6 ++--- 4 files changed, 23 insertions(+), 24 deletions(-) diff --git a/Model/lib/wdk/model/questions/params/compoundParams.xml b/Model/lib/wdk/model/questions/params/compoundParams.xml index f53765000..7f16df89e 100644 --- a/Model/lib/wdk/model/questions/params/compoundParams.xml +++ b/Model/lib/wdk/model/questions/params/compoundParams.xml @@ -309,9 +309,9 @@ lower expression in the comparator as compared to the reference. - SELECT name as term, study_id as internal, - 'Effect of pH on metabolite levels (Lewis, Baska and Llinas)' as display - FROM study.study + SELECT name as term, node_set_id as internal, + 'Effect of pH on metabolite levels (Lewis, Baska and Llinas)' as display + FROM study.nodeset WHERE name = 'Profiles of Metabolites from Llinas' @@ -323,12 +323,10 @@ lower expression in the comparator as compared to the reference. select s.name as term - , s.study_id as internal + , s.node_set_id as internal , replace(s.name, '[metaboliteProfiles]', '') as display --use display name in injector - from study.study i - , study.study s - where i.name = 'compoundMassSpec_Barrett_PurineStarvation_RSRC' - and s.investigation_id = i.study_id + from study.nodeset s + where s.name = 'compoundMassSpec_Barrett_PurineStarvation_RSRC' diff --git a/Model/lib/wdk/model/questions/params/geneParams.xml b/Model/lib/wdk/model/questions/params/geneParams.xml index 32b322762..a6334b6c8 100644 --- a/Model/lib/wdk/model/questions/params/geneParams.xml +++ b/Model/lib/wdk/model/questions/params/geneParams.xml @@ -6514,7 +6514,7 @@ products of your selected type (or types).

SELECT name AS internal, name AS term - FROM study.study + FROM study.nodeset @@ -6529,9 +6529,10 @@ products of your selected type (or types).

WHEN s.name ='MSN MetaCycle FirstStrand' THEN 'ΔMSN - Sense' WHEN s.name ='WT MetaCycle SecondStrand' THEN 'WT - Antisense' ELSE 'ΔMSN Antisense' END "term" - FROM STUDY.STUDY s, STUDY.STUDY i - Where i.name = 'ncraOR74A_Bharath_Circadian_Time_Course_ebi_rnaSeq_RSRC' - And i.study_id = s.INVESTIGATION_ID and s.name like '%MetaCycle%' + FROM STUDY.nodeset s + -- TODO: may need to join to sres.externaldatabase to filter by dataset + -- OLD: FROM STUDY.STUDY s, STUDY.STUDY i WHERE i.name = 'ncraOR74A_Bharath_Circadian_Time_Course_ebi_rnaSeq_RSRC' AND i.study_id = s.INVESTIGATION_ID and s.name like '%MetaCycle%' + Where s.name = 'ncraOR74A_Bharath_Circadian_Time_Course_ebi_rnaSeq_RSRC' @@ -6541,10 +6542,10 @@ products of your selected type (or types).

SELECT s.name as internal, REPLACE (s.name, ' MetaCycle', '') as term - FROM STUDY.STUDY s, STUDY.STUDY i - WHERE i.name = 'ncraOR74A_Hurley_2014_NC_3_ebi_rnaSeq_RSRC' - AND i.study_id = s.INVESTIGATION_ID - AND s.name like 'time course %' + FROM STUDY.nodeset s + -- TODO: may need to join to sres.externaldatabase to filter by dataset + -- OLD: FROM STUDY.STUDY s, STUDY.STUDY i WHERE i.name = 'ncraOR74A_Hurley_2014_NC_3_ebi_rnaSeq_RSRC' AND i.study_id = s.INVESTIGATION_ID AND s.name like 'time course %' + WHERE s.name = 'ncraOR74A_Hurley_2014_NC_3_ebi_rnaSeq_RSRC' @@ -6569,9 +6570,10 @@ products of your selected type (or types).

SELECT s.name as internal,s.name as term - FROM STUDY.STUDY s, STUDY.STUDY i - WHERE i.name = 'agamPEST_microarrayExpression_GSE22585_circadian_rhythm_RSRC' - AND i.study_id = s.investigation_id and s.name like '%circadian%' + FROM STUDY.nodeset s + -- TODO: may need to join to sres.externaldatabase to filter by dataset + -- OLD: FROM STUDY.STUDY s, STUDY.STUDY i WHERE i.name = 'agamPEST_microarrayExpression_GSE22585_circadian_rhythm_RSRC' AND i.study_id = s.investigation_id and s.name like '%circadian%' + WHERE s.name = 'agamPEST_microarrayExpression_GSE22585_circadian_rhythm_RSRC' diff --git a/Model/lib/wdk/model/questions/params/organismParams.xml b/Model/lib/wdk/model/questions/params/organismParams.xml index 7de643449..594606324 100644 --- a/Model/lib/wdk/model/questions/params/organismParams.xml +++ b/Model/lib/wdk/model/questions/params/organismParams.xml @@ -438,7 +438,7 @@ , SRES.TAXONNAME tn , SRES.EXTERNALDATABASE ed , SRES.EXTERNALDATABASERELEASE edr - , STUDY.STUDY s1 + , STUDY.nodeset s1 , apidb.organism o WHERE lower(d.NAME) like '%copynumbervariations_%' AND tn.TAXON_ID = d.TAXON_ID @@ -448,7 +448,6 @@ AND edr.VERSION = d.VERSION AND edr.EXTERNAL_DATABASE_ID = ed.EXTERNAL_DATABASE_ID AND s1.EXTERNAL_DATABASE_RELEASE_ID = edr.EXTERNAL_DATABASE_RELEASE_ID - AND s1.INVESTIGATION_ID is null GROUP BY tn.name ORDER BY tn.NAME diff --git a/Model/lib/wdk/model/records/geneTableQueries.xml b/Model/lib/wdk/model/records/geneTableQueries.xml index abaaee24d..7073746e1 100644 --- a/Model/lib/wdk/model/records/geneTableQueries.xml +++ b/Model/lib/wdk/model/records/geneTableQueries.xml @@ -1562,7 +1562,7 @@ from ( WHERE ga.na_feature_id = r.na_feature_id AND r.ROW_ALG_INVOCATION_ID IN ( SELECT DISTINCT s.ROW_ALG_INVOCATION_ID - FROM study.study s, sres.externaldatabase ed, sres.externaldatabaserelease edr + FROM study.nodeset s, sres.externaldatabase ed, sres.externaldatabaserelease edr WHERE ed.EXTERNAL_DATABASE_ID = edr.EXTERNAL_DATABASE_ID AND s.EXTERNAL_DATABASE_RELEASE_ID = edr.EXTERNAL_DATABASE_RELEASE_ID AND ed.name = 'pfal3D7_phenotype_pB_mutagenesis_MIS_MFS_RSRC' @@ -1584,7 +1584,7 @@ from ( where ga.na_feature_id = r.na_feature_id and r.row_alg_invocation_id in (select distinct s.row_alg_invocation_id - from study.study s, sres.externaldatabase ed, sres.externaldatabaserelease edr + from study.nodeset s, sres.externaldatabase ed, sres.externaldatabaserelease edr where ed.external_database_id = edr.external_database_id and s.external_database_release_id=edr.external_database_release_id and ed.name='pknoH_phenotype_piggyBac_mutagenesis_HME_MIS_OIS_RSRC') @@ -1609,7 +1609,7 @@ from ( where ga.na_feature_id = r.na_feature_id and r.row_alg_invocation_id in (select distinct s.row_alg_invocation_id - from study.study s, sres.externaldatabase ed, sres.externaldatabaserelease edr + from study.nodeset s, sres.externaldatabase ed, sres.externaldatabaserelease edr where ed.external_database_id = edr.external_database_id and s.external_database_release_id=edr.external_database_release_id and ed.name='pknoA1H1_phenotype_piggyBac_mutagenesis_MIS_MFS_RSRC') From a04c6072885b5fb67fc42769df67529636a27083 Mon Sep 17 00:00:00 2001 From: Cristina Aurrecoechea Date: Thu, 11 Dec 2025 09:24:08 -0500 Subject: [PATCH 14/66] we dont want to show Genetic variation section in gene pages --- Model/lib/wdk/model/records/geneRecord.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Model/lib/wdk/model/records/geneRecord.xml b/Model/lib/wdk/model/records/geneRecord.xml index af6a9b98c..ebe1d9f9a 100644 --- a/Model/lib/wdk/model/records/geneRecord.xml +++ b/Model/lib/wdk/model/records/geneRecord.xml @@ -3433,11 +3433,11 @@ name" internal="true"/> excludeProjects="EuPathDB,HostDB"> - + From 250811ea622c87ca3375f03cfb3cb900f0542f40 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Thu, 11 Dec 2025 12:14:24 -0500 Subject: [PATCH 15/66] add index to apidbtuning.transcriptattributes --- Model/lib/xml/tuningManager/apiTuningManager.xml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml index b7c2e2767..68bfe3f6b 100644 --- a/Model/lib/xml/tuningManager/apiTuningManager.xml +++ b/Model/lib/xml/tuningManager/apiTuningManager.xml @@ -41,6 +41,11 @@ CREATE UNIQUE INDEX transcriptattr_sourceId&1 ON TranscriptAttributes&1 (source_id); ]]> + + + Date: Thu, 11 Dec 2025 12:58:35 -0500 Subject: [PATCH 16/66] add ProteinAttributes tuning table --- .../lib/xml/tuningManager/apiTuningManager.xml | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml index 68bfe3f6b..11e4bc8da 100644 --- a/Model/lib/xml/tuningManager/apiTuningManager.xml +++ b/Model/lib/xml/tuningManager/apiTuningManager.xml @@ -43,7 +43,7 @@ @@ -53,6 +53,21 @@ + + + + + + + + + + + From 21fb3b3cf83c4671ba5c304fa8874023099cf177 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Thu, 11 Dec 2025 12:59:48 -0500 Subject: [PATCH 17/66] fix post cache queries --- .../model/questions/queries/geneQueries.xml | 24 +++++++------------ 1 file changed, 8 insertions(+), 16 deletions(-) diff --git a/Model/lib/wdk/model/questions/queries/geneQueries.xml b/Model/lib/wdk/model/questions/queries/geneQueries.xml index d762b635c..80ceb8d62 100644 --- a/Model/lib/wdk/model/questions/queries/geneQueries.xml +++ b/Model/lib/wdk/model/questions/queries/geneQueries.xml @@ -1320,18 +1320,15 @@ -- map any protein IDs to their transcript ID UPDATE ##WDK_CACHE_TABLE## qr SET source_id = (SELECT transcript_source_id - FROM webready.ProteinAttributes_p + FROM apidbtuning.ProteinAttributes WHERE source_id = qr.source_id - AND org_abbrev IN (%%PARTITION_KEYS%%) ) WHERE wdk_instance_id = ##WDK_CACHE_INSTANCE_ID## AND source_id in (SELECT source_id - FROM webready.ProteinAttributes_p - WHERE org_abbrev IN (%%PARTITION_KEYS%%) + FROM apidbtuning.ProteinAttributes ) AND source_id not in (SELECT source_id - FROM webready.TranscriptAttributes_p - WHERE org_abbrev IN (%%PARTITION_KEYS%%) + FROM apidbtuning.TranscriptAttributes ) ]]> @@ -1591,9 +1588,8 @@ Date: Thu, 11 Dec 2025 13:05:38 -0500 Subject: [PATCH 18/66] fix proteinattributes index --- Model/lib/xml/tuningManager/apiTuningManager.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml index 11e4bc8da..c0aa25873 100644 --- a/Model/lib/xml/tuningManager/apiTuningManager.xml +++ b/Model/lib/xml/tuningManager/apiTuningManager.xml @@ -63,7 +63,7 @@ From 8122ae971a1e2af978e10250d3db8726b7bb0c95 Mon Sep 17 00:00:00 2001 From: bindu Date: Fri, 12 Dec 2025 10:11:19 -0500 Subject: [PATCH 19/66] replace study and studylink, and deal with investigation_id --- .../wdk/model/questions/params/geneParams.xml | 47 ++++++++++++------- 1 file changed, 29 insertions(+), 18 deletions(-) diff --git a/Model/lib/wdk/model/questions/params/geneParams.xml b/Model/lib/wdk/model/questions/params/geneParams.xml index a6334b6c8..5d4c1dacb 100644 --- a/Model/lib/wdk/model/questions/params/geneParams.xml +++ b/Model/lib/wdk/model/questions/params/geneParams.xml @@ -6524,16 +6524,17 @@ products of your selected type (or types).

- SELECT s.name as internal, + SELECT s.name as internal, CASE WHEN s.name ='WT MetaCycle FirstStrand' THEN 'WT - Sense' WHEN s.name ='MSN MetaCycle FirstStrand' THEN 'ΔMSN - Sense' WHEN s.name ='WT MetaCycle SecondStrand' THEN 'WT - Antisense' ELSE 'ΔMSN Antisense' END "term" - FROM STUDY.nodeset s - -- TODO: may need to join to sres.externaldatabase to filter by dataset - -- OLD: FROM STUDY.STUDY s, STUDY.STUDY i WHERE i.name = 'ncraOR74A_Bharath_Circadian_Time_Course_ebi_rnaSeq_RSRC' AND i.study_id = s.INVESTIGATION_ID and s.name like '%MetaCycle%' - Where s.name = 'ncraOR74A_Bharath_Circadian_Time_Course_ebi_rnaSeq_RSRC' - + FROM STUDY.nodeset s, sres.externaldatabase ed, sres.externaldatabaserelease edr + WHERE ed.name = 'ncraOR74A_Bharath_Circadian_Time_Course_ebi_rnaSeq_RSRC' + AND ed.external_database_id = edr.external_database_id + AND edr.external_database_release_id = s.external_database_release_id + AND node_type IN ('RNASeq') + @@ -6541,12 +6542,17 @@ products of your selected type (or types).

- SELECT s.name as internal, REPLACE (s.name, ' MetaCycle', '') as term - FROM STUDY.nodeset s - -- TODO: may need to join to sres.externaldatabase to filter by dataset - -- OLD: FROM STUDY.STUDY s, STUDY.STUDY i WHERE i.name = 'ncraOR74A_Hurley_2014_NC_3_ebi_rnaSeq_RSRC' AND i.study_id = s.INVESTIGATION_ID AND s.name like 'time course %' - WHERE s.name = 'ncraOR74A_Hurley_2014_NC_3_ebi_rnaSeq_RSRC' - + SELECT s.name as internal, + CASE WHEN s.name ='WT MetaCycle FirstStrand' THEN 'WT - Sense' + WHEN s.name ='MSN MetaCycle FirstStrand' THEN 'ΔMSN - Sense' + WHEN s.name ='WT MetaCycle SecondStrand' THEN 'WT - Antisense' + ELSE 'ΔMSN Antisense' END "term" + FROM STUDY.nodeset s, sres.externaldatabase ed, sres.externaldatabaserelease edr + WHERE ed.name = 'ncraOR74A_Hurley_2014_NC_3_ebi_rnaSeq_RSRC' + AND ed.external_database_id = edr.external_database_id + AND edr.external_database_release_id = s.external_database_release_id + AND node_type IN ('RNASeq') + @@ -6569,12 +6575,17 @@ products of your selected type (or types).

- SELECT s.name as internal,s.name as term - FROM STUDY.nodeset s - -- TODO: may need to join to sres.externaldatabase to filter by dataset - -- OLD: FROM STUDY.STUDY s, STUDY.STUDY i WHERE i.name = 'agamPEST_microarrayExpression_GSE22585_circadian_rhythm_RSRC' AND i.study_id = s.investigation_id and s.name like '%circadian%' - WHERE s.name = 'agamPEST_microarrayExpression_GSE22585_circadian_rhythm_RSRC' - + SELECT s.name as internal, + CASE WHEN s.name ='WT MetaCycle FirstStrand' THEN 'WT - Sense' + WHEN s.name ='MSN MetaCycle FirstStrand' THEN 'ΔMSN - Sense' + WHEN s.name ='WT MetaCycle SecondStrand' THEN 'WT - Antisense' + ELSE 'ΔMSN Antisense' END "term" + FROM STUDY.nodeset s, sres.externaldatabase ed, sres.externaldatabaserelease edr + WHERE ed.name = 'agamPEST_microarrayExpression_GSE22585_circadian_rhythm_RSRC' + AND ed.external_database_id = edr.external_database_id + AND edr.external_database_release_id = s.external_database_release_id + AND node_type IN ('microarray') + From ece6cbeff46f5d3efea3e86e82ae0ed7b6feb8c2 Mon Sep 17 00:00:00 2001 From: bindu Date: Fri, 12 Dec 2025 10:12:15 -0500 Subject: [PATCH 20/66] replace study and studylink, and deal with investigation_id in DST files --- Model/lib/dst/metaCycle.dst | 9 +++++---- Model/lib/dst/rnaSeqTemplates.dst | 9 +++++---- 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/Model/lib/dst/metaCycle.dst b/Model/lib/dst/metaCycle.dst index aa386bff2..b83d54f08 100644 --- a/Model/lib/dst/metaCycle.dst +++ b/Model/lib/dst/metaCycle.dst @@ -68,11 +68,12 @@ prop=includeProjectsExcludeEuPathDB diff --git a/Model/lib/dst/rnaSeqTemplates.dst b/Model/lib/dst/rnaSeqTemplates.dst index bce0955be..2421c69fe 100644 --- a/Model/lib/dst/rnaSeqTemplates.dst +++ b/Model/lib/dst/rnaSeqTemplates.dst @@ -1154,11 +1154,12 @@ prop=includeProjectsExcludeEuPathDB From 434482ef2c40ed94846fb54a9bfd24a2e33e3809 Mon Sep 17 00:00:00 2001 From: bindu Date: Fri, 12 Dec 2025 11:17:33 -0500 Subject: [PATCH 21/66] replace study with nodeset --- Model/lib/dst/rnaSeqTemplates.dst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Model/lib/dst/rnaSeqTemplates.dst b/Model/lib/dst/rnaSeqTemplates.dst index 2421c69fe..f67119bff 100644 --- a/Model/lib/dst/rnaSeqTemplates.dst +++ b/Model/lib/dst/rnaSeqTemplates.dst @@ -734,14 +734,14 @@ SELECT study_id AS internal, ELSE ps_name || sense END AS display FROM ( - SELECT DISTINCT s.study_id as study_id + SELECT DISTINCT s.node_set_id as study_id , s.name as name , REGEXP_REPLACE (s.name, '\[(.)+\]', '') AS ps_name ,REPLACE (REPLACE ( REPLACE ( REPLACE ( REGEXP_SUBSTR (s.name, ' \[\S+ ') , 'DESeq2Analysis', '') , 'unique' , '' ), '[', '') , '-', ' ' ) AS anal ,CASE WHEN REGEXP_LIKE (s.name, '${sense}') THEN '- Sense' WHEN REGEXP_LIKE (s.name, ' ${antisense}') THEN '- Antisense' ELSE 'unstranded' END AS sense -from study.study s +from study.nodeset s , SRES.EXTERNALDATABASERELEASE r , sres.externaldatabase d where lower(s.name) like '%deseq%' From d91a89c8964c2312ff5cc4a698d94971c1edab77 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Fri, 12 Dec 2025 12:57:03 -0500 Subject: [PATCH 22/66] fix expression confidence queries --- Model/lib/dst/expression.dst | 9 --------- Model/lib/wdk/model/questions/queries/geneQueries.xml | 6 +++--- 2 files changed, 3 insertions(+), 12 deletions(-) diff --git a/Model/lib/dst/expression.dst b/Model/lib/dst/expression.dst index df08174b2..eb389c226 100644 --- a/Model/lib/dst/expression.dst +++ b/Model/lib/dst/expression.dst @@ -12,13 +12,6 @@ prop=projectName diff --git a/Model/lib/wdk/model/questions/queries/geneQueries.xml b/Model/lib/wdk/model/questions/queries/geneQueries.xml index 721b43e31..3530e5af7 100644 --- a/Model/lib/wdk/model/questions/queries/geneQueries.xml +++ b/Model/lib/wdk/model/questions/queries/geneQueries.xml @@ -4902,8 +4902,8 @@ = $$fold_change$$ @@ -4934,7 +4934,7 @@ Date: Sat, 13 Dec 2025 10:09:41 -0500 Subject: [PATCH 23/66] fix bug in apidbtuning.Profile --- Model/lib/xml/tuningManager/apiTuningManager.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml index c0aa25873..69f17c2df 100644 --- a/Model/lib/xml/tuningManager/apiTuningManager.xml +++ b/Model/lib/xml/tuningManager/apiTuningManager.xml @@ -1649,9 +1649,9 @@ create index Organism_projectId_idx&1 ON OrganismAttributes&1 (project_id, sourc na_feature_id numeric(10,0), node_type character varying(200), profile_as_string_value text, + profile_as_string_stderr text, profile_as_string_percentile1 text, - profile_as_string_percentile2 text, - profile_as_string_stderr text + profile_as_string_percentile2 text ) ]]> From dec6a7c8e44a83c086b4f1beaf5d07a19194c973 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Sun, 14 Dec 2025 09:15:43 -0500 Subject: [PATCH 24/66] use transattr tuning tbl as needed --- .../model/questions/queries/geneQueries.xml | 64 +++++++++---------- 1 file changed, 32 insertions(+), 32 deletions(-) diff --git a/Model/lib/wdk/model/questions/queries/geneQueries.xml b/Model/lib/wdk/model/questions/queries/geneQueries.xml index 3530e5af7..a42ec9e48 100644 --- a/Model/lib/wdk/model/questions/queries/geneQueries.xml +++ b/Model/lib/wdk/model/questions/queries/geneQueries.xml @@ -3269,7 +3269,7 @@ SELECT ta.gene_source_id, ta.source_id, 'Y' AS matched_result, ta.project_id , max(round(profile_min_max.max_value::numeric, 1)) AS max_percentile_chosen , min(round(profile_min_max.min_value::numeric, 1)) AS min_percentile_chosen - FROM webready.TranscriptAttributes_p ta + FROM apidbtuning.TranscriptAttributes ta , ( SELECT res.na_feature_id, res.protocol_app_node_id FROM results.NaFeatureExpression res @@ -3328,13 +3328,13 @@ , CASE WHEN (gls.LOD_SCORE_EXP = 0) THEN gls.LOD_SCORE_MANT::varchar ELSE to_char(gls.LOD_SCORE_MANT * power(10::double precision, gls.LOD_SCORE_EXP),'99.99EEEE') END AS lod_score - FROM webready.TranscriptAttributes_p ga, apidb.nafeaturehaploblock gls + FROM apidbtuning.TranscriptAttributes ga, apidb.nafeaturehaploblock gls WHERE gls.na_feature_id = ga.gene_na_feature_id AND gls.LOD_SCORE_MANT * power(10::double precision, gls.LOD_SCORE_EXP) >= $$lod_score$$ AND lower(ga.gene_source_id) != lower($$pf_gene_id$$) AND gls.HAPLOTYPE_BLOCK_NAME IN ( SELECT DISTINCT HAPLOTYPE_BLOCK_NAME - FROM webready.TranscriptAttributes_p ga, apidb.nafeaturehaploblock gls + FROM apidbtuning.TranscriptAttributes ga, apidb.nafeaturehaploblock gls WHERE gls.na_feature_id = ga.gene_na_feature_id AND lower(ga.gene_source_id) = lower($$pf_gene_id$$) AND LOD_SCORE_MANT * power(10::double precision, LOD_SCORE_EXP) >= $$lod_score$$ @@ -3343,7 +3343,7 @@ GROUP BY gene_source_id HAVING ((count(*) * 100) / ( SELECT count(*) - FROM webready.TranscriptAttributes_p ga, apidb.nafeaturehaploblock gls + FROM apidbtuning.TranscriptAttributes ga, apidb.nafeaturehaploblock gls WHERE gls.na_feature_id = ga.gene_na_feature_id AND lower(ga.gene_source_id) = lower($$pf_gene_id$$) AND LOD_SCORE_MANT * power(10::double precision, LOD_SCORE_EXP) >= $$lod_score$$ )) >= $$percentage_sim_haploblck$$ @@ -3356,7 +3356,7 @@ ELSE to_char(gls.LOD_SCORE_MANT * power(10::double precision, gls.LOD_SCORE_EXP), '99.99EEEE') END AS cut_off , ga.gene_source_id - FROM webready.TranscriptAttributes_p ga, apidb.nafeaturehaploblock gls + FROM apidbtuning.TranscriptAttributes ga, apidb.nafeaturehaploblock gls WHERE gls.na_feature_id = ga.gene_na_feature_id AND lower(ga.gene_source_id) = lower($$pf_gene_id$$) AND LOD_SCORE_MANT * power(10::double precision, LOD_SCORE_EXP) >= $$lod_score$$ @@ -3365,7 +3365,7 @@ ) b WHERE a.gene_source_id != b.gene_source_id ) q - , webready.TranscriptAttributes_p ta + , apidbtuning.TranscriptAttributes ta WHERE ta.gene_source_id = q.gene_source_id ]]> @@ -3395,7 +3395,7 @@ END AS lod_score FROM dots.chromosomeelementfeature cef , apidb.nafeaturehaploblock gls - , webready.TranscriptAttributes_p ga + , apidbtuning.TranscriptAttributes ga , dots.externalnasequence ens , dots.nalocation nl WHERE ens.source_id = $$pf_seqid$$ @@ -3472,7 +3472,7 @@ HAVING count(*) = 2 ) pan, results.NAFeatureDiffResult r, - webready.TranscriptAttributes_p t + apidbtuning.TranscriptAttributes t WHERE pan.protocol_app_node_id = r.protocol_app_node_id AND r.NA_FEATURE_ID = t.gene_na_feature_id AND r.adj_p_value <= $$adj_p_value$$ @@ -3582,7 +3582,7 @@ ELSE round(two.chosen::numeric, 2) END AS chose_group_two FROM - webready.TranscriptAttributes_p ga + apidbtuning.TranscriptAttributes ga , ( SELECT res.na_feature_id , CASE WHEN &&isLogged&& = 1 AND $$min_max_avg_comp$$ = 'minimum' @@ -3777,7 +3777,7 @@ END) END AS chose_group_two FROM - webready.TranscriptAttributes_p ga + apidbtuning.TranscriptAttributes ga , ( SELECT res.na_feature_id , CASE WHEN &&isLogged&& = 1 AND 'average' = 'minimum' @@ -3926,7 +3926,7 @@ , round($$antisense_direction$$ * log(2, REPLACE($$antisense_fold_change$$,0,0.0001)), 1) AS antisense_fold_change , round($$sense_direction$$ * log(2, REPLACE($$sense_fold_change$$,0,0.0001)), 1) AS sense_fold_change FROM - webready.TranscriptAttributes_p ga + apidbtuning.TranscriptAttributes ga , ( SELECT NA_FEATURE_ID , string_agg(sample_pair, ', ' ORDER BY NA_FEATURE_ID) AS sample_pairs @@ -4128,7 +4128,7 @@ AND pan.protocol_app_node_id = res.protocol_app_node_id GROUP BY res.na_feature_id ) two - , webready.TranscriptAttributes_p ga + , apidbtuning.TranscriptAttributes ga WHERE one.na_feature_id = two.na_feature_id AND ga.gene_na_feature_id = one.na_feature_id AND ga.gene_na_feature_id = two.na_feature_id @@ -4199,7 +4199,7 @@ , round($$antisense_direction$$ * log(2, $$antisense_fold_change$$), 1) AS antisense_fold_change , round($$sense_direction$$ * log(2, $$sense_fold_change$$), 1) AS sense_fold_change FROM - webready.TranscriptAttributes_p ga + apidbtuning.TranscriptAttributes ga , ( SELECT ref_sense_result.na_feature_id , string_agg(CONCAT(ref_sense_pan.sample, '->', comp_sense_pan.sample), ', ' @@ -4310,7 +4310,7 @@ , to_char(p_value, '9.99EEEE') AS p_value , p_value sorting_p_value FROM - webready.TranscriptAttributes_p ta + apidbtuning.TranscriptAttributes ta , ( SELECT na_feature_id , round(avg(CASE source_set WHEN 'ref' THEN linear_value END), 3) linear_avg_ref @@ -4399,7 +4399,7 @@ else linear_avg_ref end, 6) as avg_group_two, to_char( p_value, '9.99EEEE') as p_value, p_value sorting_p_value - from webready.TranscriptAttributes_p ta, + from apidbtuning.TranscriptAttributes ta, (select na_feature_id, round(avg(decode(source_set, 'ref', linear_value, null)), 3) linear_avg_ref, round(avg(decode(source_set, 'comp', linear_value, null)), 3) linear_avg_comp, @@ -4478,7 +4478,7 @@ else linear_avg_ref end, 6) as avg_group_two, to_char( p_value, '9.99EEEE') as p_value, p_value sorting_p_value - from webready.TranscriptAttributes_p ta, + from apidbtuning.TranscriptAttributes ta, (select na_feature_id, round(avg(decode(source_set, 'ref', linear_value, null)), 3) linear_avg_ref, round(avg(decode(source_set, 'comp', linear_value, null)), 3) linear_avg_comp, @@ -4553,7 +4553,7 @@ else linear_avg_ref end, 6) as avg_group_two, to_char( p_value, '9.99EEEE') as p_value, p_value sorting_p_value - from webready.TranscriptAttributes_p ta, + from apidbtuning.TranscriptAttributes ta, (select na_feature_id, round(avg(decode(source_set, 'ref', linear_value, null)), 3) linear_avg_ref, round(avg(decode(source_set, 'comp', linear_value, null)), 3) linear_avg_comp, @@ -4623,7 +4623,7 @@ else linear_avg_ref end, 6) as avg_group_two, to_char( p_value, '9.99EEEE') as p_value, p_value sorting_p_value - from webready.TranscriptAttributes_p ta, + from apidbtuning.TranscriptAttributes ta, (select na_feature_id, round(avg(decode(source_set, 'ref', linear_value, null)), 3) linear_avg_ref, round(avg(decode(source_set, 'comp', linear_value, null)), 3) linear_avg_comp, @@ -4872,7 +4872,7 @@ WHERE sl.protocol_app_node_id = pan.protocol_app_node_id AND pan.protocol_app_node_id in ($$samples_fc_ref_generic$$) AND pan.protocol_app_node_id = res.protocol_app_node_id - ) expr, webready.TranscriptAttributes_p ta + ) expr, apidbtuning.TranscriptAttributes ta WHERE ( $$protein_coding_only$$ = 'no' OR ta.gene_type = $$protein_coding_only$$ ) AND $$regulated_dir$$ (expr.fold_difference) >= $$fold_difference$$ AND ta.gene_na_feature_id = expr.gene_feature_id @@ -4904,7 +4904,7 @@ SELECT ta.source_id, ta.gene_source_id, ta.project_id, 'Y' as matched_result, round(r.fold_change::numeric, 2) as fold_change, round(r.confidence::numeric, 2) as confidence - FROM webready.TranscriptAttributes_p ta + FROM apidbtuning.TranscriptAttributes ta , results.nafeaturediffresult r WHERE $$regulated_dir$$ (r.fold_change) >= $$fold_change$$ AND r.confidence >= $$confidence$$ @@ -4936,7 +4936,7 @@ SELECT ta.source_id, ta.gene_source_id, ta.project_id, 'Y' as matched_result, round(r.fold_change::numeric, 2) as fold_change, TO_CHAR( coalesce(r.adj_p_value, r.p_value), '99.99EEEE') as pvalue - FROM webready.TranscriptAttributes_p ta + FROM apidbtuning.TranscriptAttributes ta , results.nafeaturediffresult r WHERE $$regulated_dir$$ (r.fold_change) >= $$fold_change$$ AND coalesce(r.adj_p_value, r.p_value) <= to_char($$dcc_p_value$$,'99.99999999999999') @@ -4964,7 +4964,7 @@ From dee4bf5635faab13076a69ce1a81167b3b52ec2f Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Mon, 15 Dec 2025 11:23:03 -0500 Subject: [PATCH 25/66] fix sense/antisense query --- .../wdk/model/questions/params/geneParams.xml | 2 +- .../model/questions/queries/geneQueries.xml | 20 +++++++++---------- 2 files changed, 11 insertions(+), 11 deletions(-) diff --git a/Model/lib/wdk/model/questions/params/geneParams.xml b/Model/lib/wdk/model/questions/params/geneParams.xml index 5d4c1dacb..dadce47cd 100644 --- a/Model/lib/wdk/model/questions/params/geneParams.xml +++ b/Model/lib/wdk/model/questions/params/geneParams.xml @@ -7898,7 +7898,7 @@ products of your selected type (or types).

WITH tpm AS ( - SELECT coalesce(round(power(10,10) / (num_reads * tx_length),2), 1) as value + SELECT coalesce(round((power(10,10)/(num_reads * tx_length))::numeric, 2), 1) as value FROM ( SELECT min(rs.avg_unique_reads) as num_reads, min(oa.avg_transcript_length) as tx_length FROM apidbTuning.ProfileSamples ps diff --git a/Model/lib/wdk/model/questions/queries/geneQueries.xml b/Model/lib/wdk/model/questions/queries/geneQueries.xml index a42ec9e48..50cdb37db 100644 --- a/Model/lib/wdk/model/questions/queries/geneQueries.xml +++ b/Model/lib/wdk/model/questions/queries/geneQueries.xml @@ -3876,13 +3876,13 @@ ' , comp1.sample ) as sample_pair - , round(CASE WHEN comp1.sense_value / greatest($$antisense_floor$$, ref1.sense_value) > 1 + , round((CASE WHEN comp1.sense_value / greatest($$antisense_floor$$, ref1.sense_value) > 1 THEN comp1.sense_value / greatest($$antisense_floor$$, ref1.sense_value) ELSE ref1.sense_value / greatest($$antisense_floor$$, comp1.sense_value) END @@ -3942,7 +3942,7 @@ THEN comp1.antisense_value / greatest($$antisense_floor$$, ref1.antisense_value) ELSE ref1.antisense_value / greatest($$antisense_floor$$, comp1.antisense_value) END - , 1) AS FC_product + )::numeric, 1) AS FC_product FROM comp1, ref1 WHERE ref1.NA_FEATURE_ID = comp1.NA_FEATURE_ID AND ref1.sample != comp1.sample From 9835cba4fee3c29b549131f1099c5f207ebd6f64 Mon Sep 17 00:00:00 2001 From: Ryan Doherty Date: Mon, 15 Dec 2025 13:49:55 -0500 Subject: [PATCH 26/66] Fix attributes list for EuPath --- Model/lib/wdk/model/questions/geneQuestions.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Model/lib/wdk/model/questions/geneQuestions.xml b/Model/lib/wdk/model/questions/geneQuestions.xml index 336d9c32a..792903c44 100644 --- a/Model/lib/wdk/model/questions/geneQuestions.xml +++ b/Model/lib/wdk/model/questions/geneQuestions.xml @@ -1617,7 +1617,7 @@ IMPORTANT: searchCategory="Protein Expression" queryRef="GeneId.GenesByMassSpec" recordClassRef="TranscriptRecordClasses.TranscriptRecordClass"> - From 259eb33bef345a60eea8dd77a74164541c1760f3 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Mon, 15 Dec 2025 14:33:55 -0500 Subject: [PATCH 27/66] fix rnaseq Similarity query --- Model/lib/dst/rnaSeqTemplates.dst | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/Model/lib/dst/rnaSeqTemplates.dst b/Model/lib/dst/rnaSeqTemplates.dst index f67119bff..490cc8ef5 100644 --- a/Model/lib/dst/rnaSeqTemplates.dst +++ b/Model/lib/dst/rnaSeqTemplates.dst @@ -807,13 +807,8 @@ prop=includeProjectsExcludeEuPathDB From e31b3f5673bd8098dad45ed05eb7d14705fb20ca Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Mon, 15 Dec 2025 17:22:28 -0500 Subject: [PATCH 28/66] fix cellXgene query --- Model/lib/wdk/model/questions/params/geneParams.xml | 4 +--- Model/lib/wdk/model/questions/queries/geneQueries.xml | 5 +++-- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/Model/lib/wdk/model/questions/params/geneParams.xml b/Model/lib/wdk/model/questions/params/geneParams.xml index dadce47cd..b84cc750e 100644 --- a/Model/lib/wdk/model/questions/params/geneParams.xml +++ b/Model/lib/wdk/model/questions/params/geneParams.xml @@ -6606,10 +6606,8 @@ products of your selected type (or types).

, apidbtuning.datasetdatasource dd , apidb.organism o WHERE o.abbrev = $$organismsWithSingleCell$$ - WHERE dd.taxon_id = o.taxon_id + AND dd.taxon_id = o.taxon_id AND dsp.name like '%cellxgene%' - AND dsp.name = dnt.name - AND ed.name = dnt.name AND dsp.name = ed.name AND ed.external_database_id = edr.external_database_id ]]> diff --git a/Model/lib/wdk/model/questions/queries/geneQueries.xml b/Model/lib/wdk/model/questions/queries/geneQueries.xml index 50cdb37db..4ac674e8e 100644 --- a/Model/lib/wdk/model/questions/queries/geneQueries.xml +++ b/Model/lib/wdk/model/questions/queries/geneQueries.xml @@ -5998,7 +5998,7 @@ select distinct ta.gene_source_id feature_sub.feature, ed.name AS dataset_name, 'Y' AS matched_result - FROM apidbtuning.TranscriptAttributes ta + FROM webready.TranscriptAttributes_p ta LEFT JOIN LATERAL ( SELECT cxg.source_id AS feature FROM apidb.cellxgene cxg @@ -6009,7 +6009,8 @@ select distinct ta.gene_source_id JOIN sres.externaldatabaserelease edr ON edr.external_database_release_id = $$singleCellDataset$$ JOIN sres.externaldatabase ed - ON ed.external_database_id = edr.external_database_id; + ON ed.external_database_id = edr.external_database_id + WHERE ta.org_abbrev in ($$organismsWithSingleCell$$) ]]> From ad953baac0eaf634085a265d425d02e79dd4b25a Mon Sep 17 00:00:00 2001 From: bindu Date: Tue, 16 Dec 2025 12:12:43 -0500 Subject: [PATCH 29/66] add in the internalDependency for Profile table --- Model/lib/xml/tuningManager/apiTuningManager.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml index 69f17c2df..a19b08629 100644 --- a/Model/lib/xml/tuningManager/apiTuningManager.xml +++ b/Model/lib/xml/tuningManager/apiTuningManager.xml @@ -1640,6 +1640,7 @@ create index Organism_projectId_idx&1 ON OrganismAttributes&1 (project_id, sourc + From 0623c42573f68ec94ad53059db1cabb0777d4997 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Tue, 16 Dec 2025 13:18:08 -0500 Subject: [PATCH 30/66] add index to transattr --- Model/lib/xml/tuningManager/apiTuningManager.xml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml index a19b08629..8183a1cf7 100644 --- a/Model/lib/xml/tuningManager/apiTuningManager.xml +++ b/Model/lib/xml/tuningManager/apiTuningManager.xml @@ -51,6 +51,11 @@ CREATE INDEX transcriptattr_t_p&1 ON TranscriptAttributes&1 (taxon_id, project_id, source_id); ]]> + + + From 20048ccda8b088ee983cd841ba9b8608d9e06bac Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Tue, 16 Dec 2025 13:19:17 -0500 Subject: [PATCH 31/66] speed up user comments query --- Model/lib/wdk/model/questions/queries/geneQueries.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Model/lib/wdk/model/questions/queries/geneQueries.xml b/Model/lib/wdk/model/questions/queries/geneQueries.xml index 4ac674e8e..7417c24d2 100644 --- a/Model/lib/wdk/model/questions/queries/geneQueries.xml +++ b/Model/lib/wdk/model/questions/queries/geneQueries.xml @@ -5449,7 +5449,7 @@ select distinct ta.gene_source_id ) t GROUP BY stable_id ) comm, - webready.TranscriptAttributes_p ta + apidbtuning.TranscriptAttributes ta WHERE comm.stable_id = ta.gene_source_id AND ta.org_abbrev in ($$organism_select_all$$) ]]> From e742f998fc4000126170294f506514e1132d3a6f Mon Sep 17 00:00:00 2001 From: John Brestelli Date: Wed, 17 Dec 2025 10:06:19 -0500 Subject: [PATCH 32/66] add categoryIri for wgcna (this is a temporary fix) --- .../org/apidb/apicommon/model/datasetInjector/RNASeqWGCNA.java | 3 +++ 1 file changed, 3 insertions(+) diff --git a/Model/src/main/java/org/apidb/apicommon/model/datasetInjector/RNASeqWGCNA.java b/Model/src/main/java/org/apidb/apicommon/model/datasetInjector/RNASeqWGCNA.java index 694af19b0..509cc784b 100644 --- a/Model/src/main/java/org/apidb/apicommon/model/datasetInjector/RNASeqWGCNA.java +++ b/Model/src/main/java/org/apidb/apicommon/model/datasetInjector/RNASeqWGCNA.java @@ -5,10 +5,13 @@ public class RNASeqWGCNA extends RNASeqEbi { @Override public void injectTemplates() { + setPropValue("datasetClassCategoryIri", "http://purl.obolibrary.org/obo/OBI_0001271"); super.injectTemplates(); + + injectTemplate("rnaSeqWGCNAModulesQuestion"); setPropValue("searchCategory", "searchCategory-transcriptomics-iterativeWGCNA"); setPropValue("questionName", "GeneQuestions.GenesByRNASeq" + getDatasetName() + "WGCNAModules"); From 8a829370c1af375d58e198e30f15da2e4f3c1c69 Mon Sep 17 00:00:00 2001 From: John Brestelli Date: Wed, 17 Dec 2025 12:09:59 -0500 Subject: [PATCH 33/66] make sure to set the profilegraph help as it is used in a template --- .../java/org/apidb/apicommon/model/datasetInjector/RNASeq.java | 1 + 1 file changed, 1 insertion(+) diff --git a/Model/src/main/java/org/apidb/apicommon/model/datasetInjector/RNASeq.java b/Model/src/main/java/org/apidb/apicommon/model/datasetInjector/RNASeq.java index da6c925a7..d4b892c2f 100644 --- a/Model/src/main/java/org/apidb/apicommon/model/datasetInjector/RNASeq.java +++ b/Model/src/main/java/org/apidb/apicommon/model/datasetInjector/RNASeq.java @@ -50,6 +50,7 @@ protected void setGraphYAxisDescription() { @Override public void injectTemplates() { setShortAttribution(); + setProfileSamplesHelp(); String projectName = getPropValue("projectName"); //String presenterId = getPropValue("presenterId"); From f4aa3e793ffcff61de3b27f476e4ec5b91635ff4 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Wed, 17 Dec 2025 13:33:05 -0500 Subject: [PATCH 34/66] fix eQTL query --- .../model/records/dynSpanAttributeQueries.xml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/Model/lib/wdk/model/records/dynSpanAttributeQueries.xml b/Model/lib/wdk/model/records/dynSpanAttributeQueries.xml index 51e2996a5..e47bbe145 100644 --- a/Model/lib/wdk/model/records/dynSpanAttributeQueries.xml +++ b/Model/lib/wdk/model/records/dynSpanAttributeQueries.xml @@ -56,22 +56,22 @@ SELECT ids.source_id, ids.project_id, lower(ids.project_id) as project_id_lc,ids.seq_source_id, ids.start_min, ids.end_max, ids.strand, (ids.end_max - ids.start_min + 1) AS length, - trim(to_char(ids.end_max,'999,999,999')) as end_text, - trim(to_char(ids.start_min,'999,999,999')) as start_text, - trim(to_char((ids.end_max - ids.start_min + 1),'999,999,999')) as length_text, + ids.end_max::text as end_text, + ids.start_min::text as start_text, + (ids.end_max - ids.start_min + 1)::text as length_text, sa.organism, o.public_abbrev as organismAbbrev, ids.start_min - 1000 AS context_start, ids.end_max + 1000 AS context_end FROM ( SELECT source_id, project_id, regexp_substr(source_id, '[^:]+', 1, 1) as seq_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, + regexp_substr(regexp_substr(source_id, '[^:]+', 1, 2), '[^\-]+', 1,1)::integer as start_min, + regexp_substr(regexp_substr(source_id, '[^:]+', 1, 2), '[^\-]+', 1,2)::integer as end_max, case when regexp_substr(source_id, '[^:]+', 1, 3) = 'f' then '+' when regexp_substr(source_id, '[^:]+', 1, 3) = 'r' then '-' else 'Unknown' end as strand FROM (##WDK_ID_SQL##) t ) ids - LEFT JOIN webready.GenomicSeqAttributes_p sa ON ids.seq_source_id = sa.source_id + LEFT JOIN apidbtuning.GenomicSeqAttributes sa ON ids.seq_source_id = sa.source_id INNER JOIN apidbtuning.organismattributes o ON o.organism_name = sa.organism ]]> @@ -113,7 +113,7 @@ else 'Unknown' end as strand FROM (##WDK_ID_SQL##) t ) ids - LEFT JOIN webready.GenomicSeqAttributes_p sa ON ids.seq_source_id = sa.source_id + LEFT JOIN apidbtuning.GenomicSeqAttributes sa ON ids.seq_source_id = sa.source_id INNER JOIN apidbtuning.organismattributes o ON o.organism_name = sa.organism ]]> @@ -253,4 +253,4 @@ --> - \ No newline at end of file + From 8ef2f6acbeadee6fd94a149cc26331b3e2ef9bee Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Wed, 17 Dec 2025 14:30:53 -0500 Subject: [PATCH 35/66] use unpartitioned table for bfmv --- Model/lib/wdk/model/records/transcriptAttributeQueries.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Model/lib/wdk/model/records/transcriptAttributeQueries.xml b/Model/lib/wdk/model/records/transcriptAttributeQueries.xml index 4c70ff4ef..438b58469 100644 --- a/Model/lib/wdk/model/records/transcriptAttributeQueries.xml +++ b/Model/lib/wdk/model/records/transcriptAttributeQueries.xml @@ -459,8 +459,8 @@ replace(bfmv.predicted_go_id_component, 'GO_', 'GO:') as predicted_go_id_component, replace(bfmv.predicted_go_id_function, 'GO_', 'GO:') as predicted_go_id_function, replace(bfmv.predicted_go_id_process, 'GO_', 'GO:') as predicted_go_id_process - FROM webready.TranscriptAttributes_p bfmv - WHERE bfmv.org_abbrev in (%%PARTITION_KEYS%%) + FROM apidbtuning.TranscriptAttributes bfmv + --WHERE bfmv.org_abbrev in (%%PARTITION_KEYS%%) ]]> From d9425f2e0a7cd1df899b1096dc302775cbd31591 Mon Sep 17 00:00:00 2001 From: Mustafa Nural Date: Wed, 17 Dec 2025 14:42:12 -0500 Subject: [PATCH 36/66] move org_abbrev filter out of join condition to fix partition explosion. when the filter is on the join then it's not applied to the other joins against the transcript_attributes table. --- Model/lib/psql/webready/orgSpecific/GeneAttributes_p.psql | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Model/lib/psql/webready/orgSpecific/GeneAttributes_p.psql b/Model/lib/psql/webready/orgSpecific/GeneAttributes_p.psql index bfc5e2503..3c5fd1289 100644 --- a/Model/lib/psql/webready/orgSpecific/GeneAttributes_p.psql +++ b/Model/lib/psql/webready/orgSpecific/GeneAttributes_p.psql @@ -82,8 +82,9 @@ OR d.name like '%_dbxref_uniprot_from_annotation_RSRC') ) t GROUP BY na_feature_id - ) uniprot ON ta.gene_na_feature_id = uniprot.na_feature_id and ta.org_abbrev = ':ORG_ABBREV' + ) uniprot ON ta.gene_na_feature_id = uniprot.na_feature_id LEFT JOIN :SCHEMA.GeneProduct_p gp ON ta.gene_source_id = gp.source_id and gp.org_abbrev = ':ORG_ABBREV' + WHERE ta.org_abbrev = ':ORG_ABBREV' ORDER BY ta.gene_source_id; :DECLARE_PARTITION; From 56abee815c1c3481f4bd3496d438ad2614169343 Mon Sep 17 00:00:00 2001 From: Mustafa Nural Date: Wed, 17 Dec 2025 14:45:28 -0500 Subject: [PATCH 37/66] add missing org_abbrev filter to IntronSupportLevel_p --- Model/lib/psql/webready/orgSpecific/IntronSupportLevel_p.psql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Model/lib/psql/webready/orgSpecific/IntronSupportLevel_p.psql b/Model/lib/psql/webready/orgSpecific/IntronSupportLevel_p.psql index cee0e1ba3..7fb5296e6 100644 --- a/Model/lib/psql/webready/orgSpecific/IntronSupportLevel_p.psql +++ b/Model/lib/psql/webready/orgSpecific/IntronSupportLevel_p.psql @@ -10,7 +10,7 @@ with annotatedJunctions AS ( , il.is_reversed from apidb.intronlocation il inner join :SCHEMA.TranscriptAttributes_p ta - ON il.parent_id = ta.na_feature_id + ON il.parent_id = ta.na_feature_id and ta.org_abbrev = ':ORG_ABBREV' ) group by gene_source_id ), exptJunctions as ( select gij.gene_source_id From aee928a496dfe7118826e34e83f7d2b14a17ebb5 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Wed, 17 Dec 2025 14:52:34 -0500 Subject: [PATCH 38/66] speed eQTL query --- Model/lib/wdk/model/questions/queries/spanQueries.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/Model/lib/wdk/model/questions/queries/spanQueries.xml b/Model/lib/wdk/model/questions/queries/spanQueries.xml index fd18021d1..86d993dff 100644 --- a/Model/lib/wdk/model/questions/queries/spanQueries.xml +++ b/Model/lib/wdk/model/questions/queries/spanQueries.xml @@ -409,6 +409,7 @@ and annotated_intron in ($$Intron_junction_novelty$$) AND cef.name = gls.HAPLOTYPE_BLOCK_NAME AND nl.na_feature_id = cef.na_feature_id AND cef.na_sequence_id = ens.na_sequence_id + AND ga.org_abbrev = 'pfal3D7' AND gls.LOD_SCORE_MANT * power(10::double precision, gls.LOD_SCORE_EXP) >= $$lod_score$$ ) t GROUP BY sequence_id, start_loc, end_loc From 5aa5bd981c26854ba4d3f21c76a15a2cd1502191 Mon Sep 17 00:00:00 2001 From: Bob Date: Wed, 17 Dec 2025 21:28:56 +0000 Subject: [PATCH 39/66] add Steve-ish modified HTML-structured maxRecommendedMsg --- .../wdk/model/questions/params/organismParams.xml | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/Model/lib/wdk/model/questions/params/organismParams.xml b/Model/lib/wdk/model/questions/params/organismParams.xml index 53db556aa..806ee3427 100644 --- a/Model/lib/wdk/model/questions/params/organismParams.xml +++ b/Model/lib/wdk/model/questions/params/organismParams.xml @@ -1,7 +1,20 @@ 5 - You have selected more than five organisms. This will lead to slow responses. If you can, please select fewer. Also, be sure to set your Organism Preferences for an enhanced site experience + + You are selecting more than five organisms. +

+

+ Selecting a large number of organisms may impact performance and make + results harder to interpret. +

+

+ Please select five or fewer organisms where possible. For the best experience, + use My Organism Preferences in the page header to focus on the organisms + you care about most. +

+]]> From 5ee43b5eb1f99b1d90affa1aa46fee46eaa75669 Mon Sep 17 00:00:00 2001 From: Bob Date: Wed, 17 Dec 2025 22:04:36 +0000 Subject: [PATCH 40/66] Remove quotes from value interpolations --- .../model/questions/params/organismParams.xml | 24 +++++++++---------- 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/Model/lib/wdk/model/questions/params/organismParams.xml b/Model/lib/wdk/model/questions/params/organismParams.xml index 806ee3427..d4c5351ef 100644 --- a/Model/lib/wdk/model/questions/params/organismParams.xml +++ b/Model/lib/wdk/model/questions/params/organismParams.xml @@ -76,7 +76,7 @@ "%%maxRecommendedOrganisms%%" - "%%maxRecommendedMessage%%" + %%maxRecommendedMessage%% @@ -103,7 +103,7 @@ "%%maxRecommendedOrganisms%%" - "%%maxRecommendedMessage%%" + %%maxRecommendedMessage%% @@ -132,7 +132,7 @@ "%%maxRecommendedOrganisms%%" - "%%maxRecommendedMessage%%" + %%maxRecommendedMessage%% @@ -159,7 +159,7 @@ "%%maxRecommendedOrganisms%%" - "%%maxRecommendedMessage%%" + %%maxRecommendedMessage%% @@ -185,7 +185,7 @@ "%%maxRecommendedOrganisms%%" - "%%maxRecommendedMessage%%" + %%maxRecommendedMessage%% @@ -210,7 +210,7 @@ "%%maxRecommendedOrganisms%%" - "%%maxRecommendedMessage%%" + %%maxRecommendedMessage%% @@ -267,7 +267,7 @@ "%%maxRecommendedOrganisms%%" - "%%maxRecommendedMessage%%" + %%maxRecommendedMessage%% @@ -280,7 +280,7 @@ "%%maxRecommendedOrganisms%%" - "%%maxRecommendedMessage%%" + %%maxRecommendedMessage%% @@ -305,7 +305,7 @@ "%%maxRecommendedOrganisms%%" - "%%maxRecommendedMessage%%" + %%maxRecommendedMessage%% @@ -327,7 +327,7 @@ "%%maxRecommendedOrganisms%%" - "%%maxRecommendedMessage%%" + %%maxRecommendedMessage%% @@ -341,7 +341,7 @@ "%%maxRecommendedOrganisms%%" - "%%maxRecommendedMessage%%" + %%maxRecommendedMessage%% @@ -378,7 +378,7 @@ "%%maxRecommendedOrganisms%%" - "%%maxRecommendedMessage%%" + %%maxRecommendedMessage%% From eec2e9b2e692447ff0d8c5fd33b122e9ea6ed412 Mon Sep 17 00:00:00 2001 From: Bob Date: Wed, 17 Dec 2025 22:11:24 +0000 Subject: [PATCH 41/66] try another CDATA wrapper --- .../model/questions/params/organismParams.xml | 24 +++++++++---------- 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/Model/lib/wdk/model/questions/params/organismParams.xml b/Model/lib/wdk/model/questions/params/organismParams.xml index d4c5351ef..5553b93a9 100644 --- a/Model/lib/wdk/model/questions/params/organismParams.xml +++ b/Model/lib/wdk/model/questions/params/organismParams.xml @@ -76,7 +76,7 @@ "%%maxRecommendedOrganisms%%" - %%maxRecommendedMessage%% + @@ -103,7 +103,7 @@ "%%maxRecommendedOrganisms%%" - %%maxRecommendedMessage%% + @@ -132,7 +132,7 @@ "%%maxRecommendedOrganisms%%" - %%maxRecommendedMessage%% + @@ -159,7 +159,7 @@ "%%maxRecommendedOrganisms%%" - %%maxRecommendedMessage%% + @@ -185,7 +185,7 @@ "%%maxRecommendedOrganisms%%" - %%maxRecommendedMessage%% + @@ -210,7 +210,7 @@ "%%maxRecommendedOrganisms%%" - %%maxRecommendedMessage%% + @@ -267,7 +267,7 @@ "%%maxRecommendedOrganisms%%" - %%maxRecommendedMessage%% + @@ -280,7 +280,7 @@ "%%maxRecommendedOrganisms%%" - %%maxRecommendedMessage%% + @@ -305,7 +305,7 @@ "%%maxRecommendedOrganisms%%" - %%maxRecommendedMessage%% + @@ -327,7 +327,7 @@ "%%maxRecommendedOrganisms%%" - %%maxRecommendedMessage%% + @@ -341,7 +341,7 @@ "%%maxRecommendedOrganisms%%" - %%maxRecommendedMessage%% + @@ -378,7 +378,7 @@ "%%maxRecommendedOrganisms%%" - %%maxRecommendedMessage%% + From 55bec7f6a8faf86aa7de5c8cd5bf12b01511c752 Mon Sep 17 00:00:00 2001 From: Bob Date: Wed, 17 Dec 2025 22:15:58 +0000 Subject: [PATCH 42/66] remove quotes around maxRecommended too --- .../model/questions/params/organismParams.xml | 24 +++++++++---------- 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/Model/lib/wdk/model/questions/params/organismParams.xml b/Model/lib/wdk/model/questions/params/organismParams.xml index 5553b93a9..dba0a41d4 100644 --- a/Model/lib/wdk/model/questions/params/organismParams.xml +++ b/Model/lib/wdk/model/questions/params/organismParams.xml @@ -73,7 +73,7 @@ highlightReferenceOrganisms - "%%maxRecommendedOrganisms%%" + %%maxRecommendedOrganisms%% @@ -100,7 +100,7 @@ highlightReferenceOrganisms - "%%maxRecommendedOrganisms%%" + %%maxRecommendedOrganisms%% @@ -129,7 +129,7 @@ highlightReferenceOrganisms - "%%maxRecommendedOrganisms%%" + %%maxRecommendedOrganisms%% @@ -156,7 +156,7 @@ highlightReferenceOrganisms - "%%maxRecommendedOrganisms%%" + %%maxRecommendedOrganisms%% @@ -182,7 +182,7 @@ highlightReferenceOrganisms - "%%maxRecommendedOrganisms%%" + %%maxRecommendedOrganisms%% @@ -207,7 +207,7 @@ highlightReferenceOrganisms - "%%maxRecommendedOrganisms%%" + %%maxRecommendedOrganisms%% @@ -264,7 +264,7 @@ highlightReferenceOrganisms - "%%maxRecommendedOrganisms%%" + %%maxRecommendedOrganisms%% @@ -277,7 +277,7 @@ multiPick="true" quote="true"> - "%%maxRecommendedOrganisms%%" + %%maxRecommendedOrganisms%% @@ -302,7 +302,7 @@ highlightReferenceOrganisms - "%%maxRecommendedOrganisms%%" + %%maxRecommendedOrganisms%% @@ -324,7 +324,7 @@ Select the organism(s) you wish to query. - "%%maxRecommendedOrganisms%%" + %%maxRecommendedOrganisms%% @@ -338,7 +338,7 @@ Select the organism(s) you wish to query. - "%%maxRecommendedOrganisms%%" + %%maxRecommendedOrganisms%% @@ -375,7 +375,7 @@ showOnlyPreferredOrganisms - "%%maxRecommendedOrganisms%%" + %%maxRecommendedOrganisms%% From 314af4ad6d5008aeeaa9d4533281bc6eeb0cb045 Mon Sep 17 00:00:00 2001 From: John Brestelli Date: Wed, 17 Dec 2025 22:22:06 -0500 Subject: [PATCH 43/66] update y2h Category for internal question --- Model/lib/wdk/model/questions/geneQuestions.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Model/lib/wdk/model/questions/geneQuestions.xml b/Model/lib/wdk/model/questions/geneQuestions.xml index 792903c44..3578c0074 100644 --- a/Model/lib/wdk/model/questions/geneQuestions.xml +++ b/Model/lib/wdk/model/questions/geneQuestions.xml @@ -6155,7 +6155,7 @@ Each point shows the sense fold-change and the antisense fold-change between a p - Protein interactions + Y2H interactions From 0d4fe95e8be65153198af71e5ad3adaf6d94e4d6 Mon Sep 17 00:00:00 2001 From: John Brestelli Date: Wed, 17 Dec 2025 22:28:34 -0500 Subject: [PATCH 44/66] fix other datasetCategories (quant proteomics and longreadrnaseq) --- Model/lib/wdk/model/questions/geneQuestions.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Model/lib/wdk/model/questions/geneQuestions.xml b/Model/lib/wdk/model/questions/geneQuestions.xml index 3578c0074..3805975ae 100644 --- a/Model/lib/wdk/model/questions/geneQuestions.xml +++ b/Model/lib/wdk/model/questions/geneQuestions.xml @@ -6315,7 +6315,7 @@ Each point shows the sense fold-change and the antisense fold-change between a p - LongReadRNASeq + longReadrnaseq @@ -6393,7 +6393,7 @@ Each point shows the sense fold-change and the antisense fold-change between a p - Protein expression + Protein expression (quantitative) From f29ea095d1d995cb86354b0dd703001d19891df4 Mon Sep 17 00:00:00 2001 From: Bob Date: Thu, 18 Dec 2025 08:47:17 +0000 Subject: [PATCH 45/66] Tweak organism gate message --- .../lib/wdk/model/questions/params/organismParams.xml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/Model/lib/wdk/model/questions/params/organismParams.xml b/Model/lib/wdk/model/questions/params/organismParams.xml index dba0a41d4..2144fa1c2 100644 --- a/Model/lib/wdk/model/questions/params/organismParams.xml +++ b/Model/lib/wdk/model/questions/params/organismParams.xml @@ -1,18 +1,19 @@ 5 + You are selecting more than five organisms.

- Selecting a large number of organisms may impact performance and make - results harder to interpret. + Selecting a large number of organisms may impact performance and make results harder to interpret.

- Please select five or fewer organisms where possible. For the best experience, - use My Organism Preferences in the page header to focus on the organisms - you care about most. + Please select five or fewer organisms where possible. +

+

+ For the best experience, use My Organism Preferences in the page header to focus on the organisms you care about most.

]]> From 917fa40652e97ae7d1703d702bf86b8026917f6a Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Thu, 18 Dec 2025 16:42:10 -0500 Subject: [PATCH 46/66] fix interpro attr query --- Model/lib/wdk/model/records/transcriptAttributeQueries.xml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/Model/lib/wdk/model/records/transcriptAttributeQueries.xml b/Model/lib/wdk/model/records/transcriptAttributeQueries.xml index 438b58469..862fb9b9a 100644 --- a/Model/lib/wdk/model/records/transcriptAttributeQueries.xml +++ b/Model/lib/wdk/model/records/transcriptAttributeQueries.xml @@ -459,8 +459,8 @@ replace(bfmv.predicted_go_id_component, 'GO_', 'GO:') as predicted_go_id_component, replace(bfmv.predicted_go_id_function, 'GO_', 'GO:') as predicted_go_id_function, replace(bfmv.predicted_go_id_process, 'GO_', 'GO:') as predicted_go_id_process - FROM apidbtuning.TranscriptAttributes bfmv - --WHERE bfmv.org_abbrev in (%%PARTITION_KEYS%%) + FROM webready.TranscriptAttributes_p bfmv + WHERE bfmv.org_abbrev in (%%PARTITION_KEYS%%) ]]> @@ -1695,9 +1695,8 @@ AND ta.org_abbrev in (%%PARTITION_KEYS%%) string_agg(DISTINCT interpro_primary_id, ', ') FILTER (WHERE interpro_db_name = 'SUPERFAMILY') AS superfamily_id, max(interpro_desc) FILTER (WHERE interpro_db_name = 'SUPERFAMILY') AS superfamily_description FROM webready.InterproResults_p i - RIGHT JOIN webready.TranscriptAttributes_p ta ON ta.source_id = i.transcript_source_id + RIGHT JOIN webready.TranscriptAttributes_p ta ON ta.source_id = i.transcript_source_id AND i.org_abbrev in (%%PARTITION_KEYS%%) WHERE ta.org_abbrev in (%%PARTITION_KEYS%%) - AND i.org_abbrev in (%%PARTITION_KEYS%%) GROUP BY ta.source_id, ta.gene_source_id ]]> From cb31e436915f3702201a498953e8446220c2ea3a Mon Sep 17 00:00:00 2001 From: John Brestelli Date: Thu, 18 Dec 2025 17:09:51 -0500 Subject: [PATCH 47/66] rna url query to use datasetdatasource --- Model/lib/dst/rnaSeqTemplates.dst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Model/lib/dst/rnaSeqTemplates.dst b/Model/lib/dst/rnaSeqTemplates.dst index 490cc8ef5..9dbeba248 100644 --- a/Model/lib/dst/rnaSeqTemplates.dst +++ b/Model/lib/dst/rnaSeqTemplates.dst @@ -652,7 +652,7 @@ prop=includeProjectsExcludeEuPathDB From 32192e5645a9d4d6bbedf6ed3cfe4bfa43b7d410 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Thu, 18 Dec 2025 20:04:26 -0500 Subject: [PATCH 48/66] fix pathways queries and add tuning table --- .../model/questions/queries/pathwayQueries.xml | 2 +- .../lib/wdk/model/records/pathwayTableQueries.xml | 6 +++++- Model/lib/xml/tuningManager/apiTuningManager.xml | 15 +++++++++++++++ 3 files changed, 21 insertions(+), 2 deletions(-) diff --git a/Model/lib/wdk/model/questions/queries/pathwayQueries.xml b/Model/lib/wdk/model/questions/queries/pathwayQueries.xml index 0f4de27c3..c85354552 100644 --- a/Model/lib/wdk/model/questions/queries/pathwayQueries.xml +++ b/Model/lib/wdk/model/questions/queries/pathwayQueries.xml @@ -35,7 +35,7 @@ , sres.externaldatabase ed , sres.externaldatabaserelease edr WHERE ( - p.pathway_id LIKE REPLACE(REPLACE(REPLACE(REPLACE($$metabolic_pathway_id$$,' ',''),'-', '%'),'*','%'),'any','%') + p.pathway_id::text LIKE REPLACE(REPLACE(REPLACE(REPLACE($$metabolic_pathway_id$$,' ',''),'-', '%'),'*','%'),'any','%') OR lower(p.source_id) LIKE CONCAT('%', REPLACE(REPLACE(REPLACE(REPLACE(lower($$pathway_wildcard$$),' ',''),'-', '%'),'*','%'),'any','%'), '%') OR lower(p.name) LIKE CONCAT('%', REPLACE(REPLACE(REPLACE(REPLACE(lower($$pathway_wildcard$$),' ',''),'-', '%'),'*','%'),'any','%'), '%') ) diff --git a/Model/lib/wdk/model/records/pathwayTableQueries.xml b/Model/lib/wdk/model/records/pathwayTableQueries.xml index 6cfbd1e9d..2f2bee73f 100644 --- a/Model/lib/wdk/model/records/pathwayTableQueries.xml +++ b/Model/lib/wdk/model/records/pathwayTableQueries.xml @@ -37,18 +37,22 @@ , pr.PRODUCTS_TEXT , CASE WHEN pr.ENZYME = '-.-.-.-' THEN 'N/A' - ELSE CONCAT('', pn.GENE_COUNT, '') + ELSE CONCAT('', gc.GENE_COUNT, '') END AS GENE_COUNT FROM webready.PathwayAttributes pa , webready.PathwayCompounds pc , webready.PathwayReactions pr , webready.PathwayNodes pn + , (select pathway_source_id, count(gene_source_id) as gene_count + from apidbtuning.PathwayGenesThin + group by pathway_source_id) as gc WHERE pc.pathway_id = pa.PATHWAY_ID AND pn.SOURCE_ID = pa.SOURCE_ID AND pr.REACTION_ID = pc.REACTION_ID AND pr.EXT_DB_NAME = pc.EXT_DB_NAME AND pr.ENZYME = pn.DISPLAY_LABEL + AND gc.pathway_source_id = pa.source_id ORDER BY pr.ENZYME ]]> diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml index 8183a1cf7..f7759861b 100644 --- a/Model/lib/xml/tuningManager/apiTuningManager.xml +++ b/Model/lib/xml/tuningManager/apiTuningManager.xml @@ -103,6 +103,21 @@ + + + + + + + + + + + From 115fd3a9358f5000f83a4fba52a63724f91a66b0 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Thu, 18 Dec 2025 20:18:27 -0500 Subject: [PATCH 49/66] filter on project_id --- Model/lib/wdk/model/records/transcriptAttributeQueries.xml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/Model/lib/wdk/model/records/transcriptAttributeQueries.xml b/Model/lib/wdk/model/records/transcriptAttributeQueries.xml index 862fb9b9a..84f343b0a 100644 --- a/Model/lib/wdk/model/records/transcriptAttributeQueries.xml +++ b/Model/lib/wdk/model/records/transcriptAttributeQueries.xml @@ -96,8 +96,9 @@ ta.project_id AS project_id, ta.gene_source_id, a.ID as old_gene_source_id, ta.source_id as old_source_id, ta.project_id AS old_project_id - FROM webready.GeneId_p a, webready.TranscriptAttributes_p ta + FROM webready.GeneId_p a, apidbtuning.TranscriptAttributes ta WHERE ta.gene_source_id = a.gene + AND (ta.project_id = '@PROJECT_ID@' or 'UniDB' = '@PROJECT_ID@') -- AND a.unique_mapping = 1 ]]> @@ -112,7 +113,8 @@ SELECT ta.source_id, ta.gene_source_id, ta.project_id AS project_id - FROM webready.TranscriptAttributes_p ta + FROM apidbtuning.TranscriptAttributes ta + AND (ta.project_id = '@PROJECT_ID@' or 'UniDB' = '@PROJECT_ID@') ]]> From ab276ff95a67a0c1124c7a01588f5ab1a7b30be8 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Thu, 18 Dec 2025 20:30:05 -0500 Subject: [PATCH 50/66] fix PathwayGenes TT --- Model/lib/xml/tuningManager/apiTuningManager.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml index f7759861b..b850e6dcd 100644 --- a/Model/lib/xml/tuningManager/apiTuningManager.xml +++ b/Model/lib/xml/tuningManager/apiTuningManager.xml @@ -108,12 +108,12 @@ From 9edf93d6ea587968247495875ba22ccabcd5beec Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Thu, 18 Dec 2025 21:03:47 -0500 Subject: [PATCH 51/66] speed gene seq table query --- Model/lib/wdk/model/records/geneTableQueries.xml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/Model/lib/wdk/model/records/geneTableQueries.xml b/Model/lib/wdk/model/records/geneTableQueries.xml index 7073746e1..842fb67c8 100644 --- a/Model/lib/wdk/model/records/geneTableQueries.xml +++ b/Model/lib/wdk/model/records/geneTableQueries.xml @@ -4430,11 +4430,14 @@ where org_abbrev in (%%PARTITION_KEYS%%) FROM webready.TranscriptAttributes_p ta INNER JOIN webready.TranscriptSequence_p tx_seq ON ta.source_id = tx_seq.source_id + AND tx_seq.org_abbrev IN (%%PARTITION_KEYS%%) INNER JOIN webready.TranscriptGenomicSequence_p gseq ON ta.source_id = gseq.source_id + AND gseq.org_abbrev IN (%%PARTITION_KEYS%%) LEFT JOIN webready.ProteinSequence_p ps ON ta.protein_source_id = ps.source_id + AND ps.org_abbrev IN (%%PARTITION_KEYS%%) LEFT JOIN webready.IntronUtrCoords_p iuc ON ta.na_feature_id = iuc.na_feature_id + AND iuc.org_abbrev IN (%%PARTITION_KEYS%%) WHERE ta.org_abbrev IN (%%PARTITION_KEYS%%) - AND gseq.org_abbrev IN (%%PARTITION_KEYS%%) ]]> From 20d71e5909deb0caedc1cf18594e0771bf38771a Mon Sep 17 00:00:00 2001 From: John Brestelli Date: Fri, 19 Dec 2025 09:17:50 -0500 Subject: [PATCH 52/66] gene source_id and project not being returned correctly. fixes nc rna gene pages --- Model/lib/wdk/model/records/geneAttributeQueries.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Model/lib/wdk/model/records/geneAttributeQueries.xml b/Model/lib/wdk/model/records/geneAttributeQueries.xml index 3fa90a214..c47019d61 100644 --- a/Model/lib/wdk/model/records/geneAttributeQueries.xml +++ b/Model/lib/wdk/model/records/geneAttributeQueries.xml @@ -178,8 +178,8 @@ WHERE ga.org_abbrev IN (%%PARTITION_KEYS%%) Date: Fri, 19 Dec 2025 17:03:46 -0500 Subject: [PATCH 53/66] comment out postCacheUpdateSql --- Model/lib/wdk/model/questions/queries/geneQueries.xml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/Model/lib/wdk/model/questions/queries/geneQueries.xml b/Model/lib/wdk/model/questions/queries/geneQueries.xml index 7417c24d2..a5ae4205a 100644 --- a/Model/lib/wdk/model/questions/queries/geneQueries.xml +++ b/Model/lib/wdk/model/questions/queries/geneQueries.xml @@ -2,11 +2,11 @@ - + diff --git a/Model/lib/wdk/model/questions/geneQuestions.xml b/Model/lib/wdk/model/questions/geneQuestions.xml index 3805975ae..e7df83412 100644 --- a/Model/lib/wdk/model/questions/geneQuestions.xml +++ b/Model/lib/wdk/model/questions/geneQuestions.xml @@ -2507,7 +2507,7 @@ Find genes based on the Gene Ontology (GO) Term(s) or ID(s) assigned to them. - - - - + @@ -289,7 +289,7 @@ lower expression in the comparator as compared to the reference. - + diff --git a/Model/lib/wdk/model/questions/params/geneParams.xml b/Model/lib/wdk/model/questions/params/geneParams.xml index b84cc750e..f2c1c0c74 100644 --- a/Model/lib/wdk/model/questions/params/geneParams.xml +++ b/Model/lib/wdk/model/questions/params/geneParams.xml @@ -208,7 +208,7 @@ --> -
- + diff --git a/Model/lib/wdk/model/questions/params/organismParams.xml b/Model/lib/wdk/model/questions/params/organismParams.xml index 2144fa1c2..ea720c90b 100644 --- a/Model/lib/wdk/model/questions/params/organismParams.xml +++ b/Model/lib/wdk/model/questions/params/organismParams.xml @@ -383,7 +383,7 @@ - - + diff --git a/Model/lib/wdk/model/questions/params/pathwayParams.xml b/Model/lib/wdk/model/questions/params/pathwayParams.xml index cdfb642a9..ff2b4d3c3 100644 --- a/Model/lib/wdk/model/questions/params/pathwayParams.xml +++ b/Model/lib/wdk/model/questions/params/pathwayParams.xml @@ -1,6 +1,6 @@ - + - + diff --git a/Model/lib/wdk/model/questions/pathwayQuestions.xml b/Model/lib/wdk/model/questions/pathwayQuestions.xml index 602fea139..4f106cd59 100644 --- a/Model/lib/wdk/model/questions/pathwayQuestions.xml +++ b/Model/lib/wdk/model/questions/pathwayQuestions.xml @@ -1,7 +1,7 @@ + displayName="Search for Metabolic Pathways"> diff --git a/Model/lib/wdk/model/questions/queries/compoundQueries.xml b/Model/lib/wdk/model/questions/queries/compoundQueries.xml index 1c457c017..cbc7f1c86 100644 --- a/Model/lib/wdk/model/questions/queries/compoundQueries.xml +++ b/Model/lib/wdk/model/questions/queries/compoundQueries.xml @@ -1,6 +1,5 @@ - + diff --git a/Model/lib/wdk/model/questions/queries/geneQueries.xml b/Model/lib/wdk/model/questions/queries/geneQueries.xml index c268ca35c..6978e2f90 100644 --- a/Model/lib/wdk/model/questions/queries/geneQueries.xml +++ b/Model/lib/wdk/model/questions/queries/geneQueries.xml @@ -4937,7 +4937,7 @@ FROM apidbtuning.TranscriptAttributes ta , results.nafeaturediffresult r WHERE $$regulated_dir$$ (r.fold_change) >= $$fold_change$$ - AND coalesce(r.adj_p_value, r.p_value) <= to_char($$dcc_p_value$$,'99.99999999999999') + AND coalesce(r.adj_p_value, r.p_value) <= $$dcc_p_value$$ AND r.protocol_app_node_id = $$samples_direct_generic_confidence$$ AND ta.gene_na_feature_id = r.na_feature_id AND ( $$protein_coding_only$$ = 'no' OR ta.gene_type = $$protein_coding_only$$ ) @@ -5521,7 +5521,7 @@ select distinct ta.gene_source_id - + @@ -5586,7 +5586,7 @@ select distinct ta.gene_source_id - + @@ -5978,7 +5978,7 @@ select distinct ta.gene_source_id - + diff --git a/Model/lib/wdk/model/questions/queries/pathwayQueries.xml b/Model/lib/wdk/model/questions/queries/pathwayQueries.xml index c85354552..54b84a9a4 100644 --- a/Model/lib/wdk/model/questions/queries/pathwayQueries.xml +++ b/Model/lib/wdk/model/questions/queries/pathwayQueries.xml @@ -1,5 +1,5 @@ - + @@ -67,7 +67,7 @@ AS (select pathway_source from ($$ds_pathway_id$$)) SELECT source_id, pathway_source, string_agg(identifier, ',') as identifiers, - string_agg(type, ',') as type, + string_agg(type, ',') as type FROM ( -- Compounds SELECT distinct pa.source_id as source_id diff --git a/Model/lib/wdk/model/questions/queries/spanQueries.xml b/Model/lib/wdk/model/questions/queries/spanQueries.xml index 86d993dff..4da26f8e7 100644 --- a/Model/lib/wdk/model/questions/queries/spanQueries.xml +++ b/Model/lib/wdk/model/questions/queries/spanQueries.xml @@ -125,7 +125,7 @@ , lrt.transcript_novelty FROM apidb.longreadtranscript lrt , JSON_TABLE(count_data, '$.*' COLUMNS (reads INTEGER PATH '$')) count_table - , webready.GenomicSeqAttributes_p gsa + , apidbtuning.GenomicSeqAttributes gsa , sres.externaldatabase ed , sres.externaldatabaserelease edr , apidbtuning.organismattributes oa diff --git a/Model/lib/wdk/model/questions/spanQuestions.xml b/Model/lib/wdk/model/questions/spanQuestions.xml index d5425d0ee..04b422f98 100644 --- a/Model/lib/wdk/model/questions/spanQuestions.xml +++ b/Model/lib/wdk/model/questions/spanQuestions.xml @@ -585,7 +585,7 @@ doi:10.1371/journal.pbio.0060238 @@ -609,7 +609,7 @@ doi:10.1371/journal.pbio.0060238 - LongReadRNASeq + longReadrnaseq diff --git a/Model/lib/wdk/model/records/compoundAttributeQueries.xml b/Model/lib/wdk/model/records/compoundAttributeQueries.xml index cea95f737..005962491 100644 --- a/Model/lib/wdk/model/records/compoundAttributeQueries.xml +++ b/Model/lib/wdk/model/records/compoundAttributeQueries.xml @@ -1,5 +1,5 @@ - + CID:93072 diff --git a/Model/lib/wdk/model/records/compoundRecord.xml b/Model/lib/wdk/model/records/compoundRecord.xml index 3bdb64621..dea506852 100644 --- a/Model/lib/wdk/model/records/compoundRecord.xml +++ b/Model/lib/wdk/model/records/compoundRecord.xml @@ -1,5 +1,5 @@ - + diff --git a/Model/lib/wdk/model/records/compoundTableQueries.xml b/Model/lib/wdk/model/records/compoundTableQueries.xml index 6b5ec7920..e7db24f43 100644 --- a/Model/lib/wdk/model/records/compoundTableQueries.xml +++ b/Model/lib/wdk/model/records/compoundTableQueries.xml @@ -1,5 +1,5 @@ - + CID:93072 diff --git a/Model/lib/wdk/model/records/pathwayAttributeQueries.xml b/Model/lib/wdk/model/records/pathwayAttributeQueries.xml index 5ef350790..d7452a0a9 100644 --- a/Model/lib/wdk/model/records/pathwayAttributeQueries.xml +++ b/Model/lib/wdk/model/records/pathwayAttributeQueries.xml @@ -1,5 +1,5 @@ - + ec00626 diff --git a/Model/lib/wdk/model/records/pathwayRecord.xml b/Model/lib/wdk/model/records/pathwayRecord.xml index df05f3cb3..746c9798c 100644 --- a/Model/lib/wdk/model/records/pathwayRecord.xml +++ b/Model/lib/wdk/model/records/pathwayRecord.xml @@ -1,5 +1,5 @@ - + diff --git a/Model/lib/wdk/model/records/pathwayTableQueries.xml b/Model/lib/wdk/model/records/pathwayTableQueries.xml index 2f2bee73f..f076d094f 100644 --- a/Model/lib/wdk/model/records/pathwayTableQueries.xml +++ b/Model/lib/wdk/model/records/pathwayTableQueries.xml @@ -1,6 +1,6 @@ - + ec00626 From 2b7ce40c87361a2174d7874a027de3fad9d161da Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Mon, 5 Jan 2026 12:47:20 -0500 Subject: [PATCH 58/66] fix oracle-specific sql --- .../lib/wdk/model/questions/geneQuestions.xml | 2 +- .../records/transcriptAttributeQueries.xml | 211 +++++++++++++----- .../wdk/model/records/transcriptRecord.xml | 6 +- Model/lib/xml/dataPlotter/queries.xml | 10 +- 4 files changed, 157 insertions(+), 72 deletions(-) diff --git a/Model/lib/wdk/model/questions/geneQuestions.xml b/Model/lib/wdk/model/questions/geneQuestions.xml index e7df83412..7a62cc045 100644 --- a/Model/lib/wdk/model/questions/geneQuestions.xml +++ b/Model/lib/wdk/model/questions/geneQuestions.xml @@ -6291,7 +6291,7 @@ Each point shows the sense fold-change and the antisense fold-change between a p diff --git a/Model/lib/wdk/model/records/transcriptAttributeQueries.xml b/Model/lib/wdk/model/records/transcriptAttributeQueries.xml index 6f0bfc01f..33f69815c 100644 --- a/Model/lib/wdk/model/records/transcriptAttributeQueries.xml +++ b/Model/lib/wdk/model/records/transcriptAttributeQueries.xml @@ -128,7 +128,7 @@ @@ -1706,7 +1705,7 @@ AND ta.org_abbrev in (%%PARTITION_KEYS%%) - + @@ -1721,39 +1720,83 @@ AND ta.org_abbrev in (%%PARTITION_KEYS%%) = 1 THEN round(greatest(1,bfd3_cds) / greatest(1,no_tet_cds), 1) - ELSE round(-1 * greatest(1,no_tet_cds) / greatest(1,bfd3_cds), 1) END, - CASE WHEN (bfd3_cds < 1 or no_tet_cds < 1) then '*' else '' END) AS fc_bfd3_cds - , CONCAT(CASE WHEN greatest(1,bfd6_cds) / greatest(1,no_tet_cds) >= 1 THEN round(greatest(1,bfd6_cds) / greatest(1,no_tet_cds), 1) - ELSE round(-1 * greatest(1,no_tet_cds) / greatest(1,bfd6_cds), 1) END, - CASE WHEN (bfd6_cds < 1 or no_tet_cds < 1) then '*' else '' END) AS fc_bfd6_cds - , CONCAT(CASE WHEN greatest(1,pf_cds) / greatest(1,no_tet_cds) >= 1 THEN round(greatest(1,pf_cds) / greatest(1,no_tet_cds), 1) - ELSE round(-1 * greatest(1,no_tet_cds) / greatest(1,pf_cds), 1) END, - CASE WHEN (pf_cds < 1 or no_tet_cds < 1) then '*' else '' END) AS fc_pf_cds - , CONCAT(CASE WHEN greatest(1,dif_cds) / greatest(1,no_tet_cds) >= 1 THEN round(greatest(1,dif_cds) / greatest(1,no_tet_cds), 1) - else round(-1 * greatest(1,no_tet_cds) / greatest(1,dif_cds), 1) end, - case when (dif_cds < 1 or no_tet_cds < 1) then '*' else '' end) as fc_dif_cds - FROM webready.TranscriptAttributes_p ta, ( - select ta.gene_source_id as gene_id, ps.protocol_app_node_name, round(nfe.value,2) as value - from apidbtuning.profilesamples ps, results.nafeatureexpression nfe, webready.TranscriptAttributes_p ta - where ps.study_name = 'T.brucei paired end RNA Seq data from Horn aligned with cds coordinates [htseq-union - unstranded - tpm - unique]' - and ps.protocol_app_node_id = nfe.protocol_app_node_id - and ps.profile_type='values' - and ps.protocol_app_node_id = nfe.protocol_app_node_id - and ta.gene_na_feature_id = nfe.na_feature_id(+) - AND ta.org_abbrev IN (%%PARTITION_KEYS%%) - ) pivot ( - max(value) as cds - for protocol_app_node_name in ('No_Tet' no_tet, 'BFD3' bfd3, 'BFD6' bfd6, 'PF' pf, 'DIF' dif) - ) res - WHERE ta.gene_source_id = res.gene_id (+) - AND ta.org_abbrev in (%%PARTITION_KEYS%%) +SELECT + ta.source_id, + ta.gene_source_id, + ta.project_id, + res.*, + + CONCAT( + CASE + WHEN greatest(1, bfd3_cds) / greatest(1, no_tet_cds) >= 1 + THEN round(greatest(1, bfd3_cds) / greatest(1, no_tet_cds), 1) + ELSE + round(-1 * greatest(1, no_tet_cds) / greatest(1, bfd3_cds), 1) + END, + CASE WHEN (bfd3_cds < 1 OR no_tet_cds < 1) THEN '*' ELSE '' END + ) AS fc_bfd3_cds, + + CONCAT( + CASE + WHEN greatest(1, bfd6_cds) / greatest(1, no_tet_cds) >= 1 + THEN round(greatest(1, bfd6_cds) / greatest(1, no_tet_cds), 1) + ELSE + round(-1 * greatest(1, no_tet_cds) / greatest(1, bfd6_cds), 1) + END, + CASE WHEN (bfd6_cds < 1 OR no_tet_cds < 1) THEN '*' ELSE '' END + ) AS fc_bfd6_cds, + + CONCAT( + CASE + WHEN greatest(1, pf_cds) / greatest(1, no_tet_cds) >= 1 + THEN round(greatest(1, pf_cds) / greatest(1, no_tet_cds), 1) + ELSE + round(-1 * greatest(1, no_tet_cds) / greatest(1, pf_cds), 1) + END, + CASE WHEN (pf_cds < 1 OR no_tet_cds < 1) THEN '*' ELSE '' END + ) AS fc_pf_cds, + + CONCAT( + CASE + WHEN greatest(1, dif_cds) / greatest(1, no_tet_cds) >= 1 + THEN round(greatest(1, dif_cds) / greatest(1, no_tet_cds), 1) + ELSE + round(-1 * greatest(1, no_tet_cds) / greatest(1, dif_cds), 1) + END, + CASE WHEN (dif_cds < 1 OR no_tet_cds < 1) THEN '*' ELSE '' END + ) AS fc_dif_cds + +FROM webready.transcriptattributes_p ta + +LEFT JOIN ( + SELECT + ta.gene_source_id AS gene_id, + + MAX(value::numeric) FILTER (WHERE protocol_app_node_name = 'No_Tet') AS no_tet_cds, + MAX(value::numeric) FILTER (WHERE protocol_app_node_name = 'BFD3') AS bfd3_cds, + MAX(value::numeric) FILTER (WHERE protocol_app_node_name = 'BFD6') AS bfd6_cds, + MAX(value::numeric) FILTER (WHERE protocol_app_node_name = 'PF') AS pf_cds, + MAX(value::numeric) FILTER (WHERE protocol_app_node_name = 'DIF') AS dif_cds + + FROM apidbtuning.profilesamples ps + JOIN results.nafeatureexpression nfe + ON ps.protocol_app_node_id = nfe.protocol_app_node_id + JOIN webready.transcriptattributes_p ta + ON ta.gene_na_feature_id = nfe.na_feature_id + WHERE ps.study_name = + 'T.brucei paired end RNA Seq data from Horn aligned with cds coordinates [htseq-union - unstranded - tpm - unique]' + AND ps.profile_type = 'values' + AND ta.org_abbrev IN (%%PARTITION_KEYS%%) + GROUP BY ta.gene_source_id +) res +ON ta.gene_source_id = res.gene_id + +WHERE ta.org_abbrev IN (%%PARTITION_KEYS%%) ]]> - + @@ -1768,34 +1811,78 @@ AND ta.org_abbrev in (%%PARTITION_KEYS%%) = 1 THEN round(greatest(1,bfd3_model) / greatest(1,no_tet_model), 1) - ELSE round(-1 * greatest(1,no_tet_model) / greatest(1,bfd3_model), 1) END, - CASE WHEN (bfd3_model < 1 or no_tet_model < 1) then '*' else '' END) AS fc_bfd3_model - , CONCAT(CASE WHEN greatest(1,bfd6_model) / greatest(1,no_tet_model) >= 1 THEN round(greatest(1,bfd6_model) / greatest(1,no_tet_model), 1) - ELSE round(-1 * greatest(1,no_tet_model) / greatest(1,bfd6_model), 1) END, - CASE WHEN (bfd6_model < 1 or no_tet_model < 1) then '*' else '' END) AS fc_bfd6_model - , CONCAT(CASE WHEN greatest(1,pf_model) / greatest(1,no_tet_model) >= 1 THEN round(greatest(1,pf_model) / greatest(1,no_tet_model), 1) - ELSE round(-1 * greatest(1,no_tet_model) / greatest(1,pf_model), 1) END, - CASE WHEN (pf_model < 1 or no_tet_model < 1) then '*' else '' END) AS fc_pf_model - , CONCAT(CASE WHEN greatest(1,dif_model) / greatest(1,no_tet_model) >= 1 THEN round(greatest(1,dif_model) / greatest(1,no_tet_model), 1) - else round(-1 * greatest(1,no_tet_model) / greatest(1,dif_model), 1) end, - case when (dif_model < 1 or no_tet_model < 1) then '*' else '' end) as fc_dif_model - FROM webready.TranscriptAttributes_p ta, ( - select ta.gene_source_id as gene_id, ps.protocol_app_node_name, round(nfe.value,2) as value - from apidbtuning.profilesamples ps, results.nafeatureexpression nfe, webready.TranscriptAttributes_p ta - where ps.study_name = 'T.brucei paired end RNA Seq data from Horn [htseq-union - unstranded - tpm - unique]' - and ps.protocol_app_node_id = nfe.protocol_app_node_id - and ps.profile_type='values' - and ps.protocol_app_node_id = nfe.protocol_app_node_id - and ta.gene_na_feature_id = nfe.na_feature_id(+) - AND ta.org_abbrev IN (%%PARTITION_KEYS%%) - ) pivot ( - max(value) as model - for protocol_app_node_name in ('No_Tet' no_tet, 'BFD3' bfd3, 'BFD6' bfd6, 'PF' pf, 'DIF' dif) - ) res - WHERE ta.gene_source_id = res.gene_id (+) - AND ta.org_abbrev in (%%PARTITION_KEYS%%) +SELECT + ta.source_id, + ta.gene_source_id, + ta.project_id, + res.*, + + CONCAT( + CASE + WHEN greatest(1, bfd3_model) / greatest(1, no_tet_model) >= 1 + THEN round((greatest(1, bfd3_model)::numeric / greatest(1, no_tet_model)::numeric), 1) + ELSE + round((-1 * greatest(1, no_tet_model)::numeric / greatest(1, bfd3_model)::numeric), 1) + END, + CASE WHEN (bfd3_model < 1 OR no_tet_model < 1) THEN '*' ELSE '' END + ) AS fc_bfd3_model, + + CONCAT( + CASE + WHEN greatest(1, bfd6_model) / greatest(1, no_tet_model) >= 1 + THEN round((greatest(1, bfd6_model)::numeric / greatest(1, no_tet_model)::numeric), 1) + ELSE + round((-1 * greatest(1, no_tet_model)::numeric / greatest(1, bfd6_model)::numeric), 1) + END, + CASE WHEN (bfd6_model < 1 OR no_tet_model < 1) THEN '*' ELSE '' END + ) AS fc_bfd6_model, + + CONCAT( + CASE + WHEN greatest(1, pf_model) / greatest(1, no_tet_model) >= 1 + THEN round((greatest(1, pf_model)::numeric / greatest(1, no_tet_model)::numeric), 1) + ELSE + round((-1 * greatest(1, no_tet_model)::numeric / greatest(1, pf_model)::numeric), 1) + END, + CASE WHEN (pf_model < 1 OR no_tet_model < 1) THEN '*' ELSE '' END + ) AS fc_pf_model, + + CONCAT( + CASE + WHEN greatest(1, dif_model) / greatest(1, no_tet_model) >= 1 + THEN round((greatest(1, dif_model)::numeric / greatest(1, no_tet_model)::numeric), 1) + ELSE + round((-1 * greatest(1, no_tet_model)::numeric / greatest(1, dif_model)::numeric), 1) + END, + CASE WHEN (dif_model < 1 OR no_tet_model < 1) THEN '*' ELSE '' END + ) AS fc_dif_model + +FROM webready.transcriptattributes_p ta + +LEFT JOIN ( + SELECT + ta.gene_source_id AS gene_id, + + MAX(value::numeric) FILTER (WHERE protocol_app_node_name = 'No_Tet') AS no_tet_model, + MAX(value::numeric) FILTER (WHERE protocol_app_node_name = 'BFD3') AS bfd3_model, + MAX(value::numeric) FILTER (WHERE protocol_app_node_name = 'BFD6') AS bfd6_model, + MAX(value::numeric) FILTER (WHERE protocol_app_node_name = 'PF') AS pf_model, + MAX(value::numeric) FILTER (WHERE protocol_app_node_name = 'DIF') AS dif_model + + FROM apidbtuning.profilesamples ps + JOIN results.nafeatureexpression nfe + ON ps.protocol_app_node_id = nfe.protocol_app_node_id + JOIN webready.transcriptattributes_p ta + ON ta.gene_na_feature_id = nfe.na_feature_id + WHERE ps.study_name = + 'T.brucei paired end RNA Seq data from Horn [htseq-union - unstranded - tpm - unique]' + AND ps.profile_type = 'values' + AND ta.org_abbrev IN (%%PARTITION_KEYS) + GROUP BY ta.gene_source_id +) res +ON ta.gene_source_id = res.gene_id + +WHERE ta.org_abbrev IN (%%PARTITION_KEYS%%); ]]> diff --git a/Model/lib/wdk/model/records/transcriptRecord.xml b/Model/lib/wdk/model/records/transcriptRecord.xml index 5ecafdc94..f5c1c4993 100644 --- a/Model/lib/wdk/model/records/transcriptRecord.xml +++ b/Model/lib/wdk/model/records/transcriptRecord.xml @@ -1187,8 +1187,7 @@ - diff --git a/Model/lib/xml/dataPlotter/queries.xml b/Model/lib/xml/dataPlotter/queries.xml index 40f8688f0..fae593b61 100644 --- a/Model/lib/xml/dataPlotter/queries.xml +++ b/Model/lib/xml/dataPlotter/queries.xml @@ -70,16 +70,16 @@ Date: Tue, 6 Jan 2026 21:59:54 -0500 Subject: [PATCH 59/66] Comply with new SQLRunner API --- .../java/org/apidb/apicommon/model/maintain/BasketFixer2.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Model/src/main/java/org/apidb/apicommon/model/maintain/BasketFixer2.java b/Model/src/main/java/org/apidb/apicommon/model/maintain/BasketFixer2.java index 0640b52a4..a35badebf 100644 --- a/Model/src/main/java/org/apidb/apicommon/model/maintain/BasketFixer2.java +++ b/Model/src/main/java/org/apidb/apicommon/model/maintain/BasketFixer2.java @@ -17,8 +17,8 @@ import org.apache.log4j.Logger; import org.gusdb.fgputil.BaseCLI; import org.gusdb.fgputil.db.SqlUtils; -import org.gusdb.fgputil.db.runner.BasicResultSetHandler; import org.gusdb.fgputil.db.runner.SQLRunner; +import org.gusdb.fgputil.db.runner.handler.BasicResultSetHandler; import org.gusdb.wdk.model.Utilities; import org.gusdb.wdk.model.WdkModel; import org.gusdb.wdk.model.WdkModelException; @@ -306,7 +306,7 @@ private void updateTranscripts(WdkModel wdkModel, String projectId) throws WdkMo // get a snapshot of largest basket id. any newer ids are added by users during this run. we can ignore them. String sql = "select max(basket_id) as max_basket_id from " + userSchema + "user_baskets"; BasicResultSetHandler handler = new SQLRunner(userDbDataSource, sql, - "invalid-step-report-summary").executeQuery(new Object[]{}, new BasicResultSetHandler()); + "invalid-step-report-summary").executeQuery(new BasicResultSetHandler()); List> results = handler.getResults(); Map row = results.get(0); BigDecimal maxBasketId = (BigDecimal)row.get("MAX_BASKET_ID"); From 601087c562c6847e74ae51bb87e6bb6064929ed8 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Wed, 7 Jan 2026 10:34:35 -0500 Subject: [PATCH 60/66] fix typo bug --- Model/lib/wdk/model/records/transcriptAttributeQueries.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Model/lib/wdk/model/records/transcriptAttributeQueries.xml b/Model/lib/wdk/model/records/transcriptAttributeQueries.xml index 33f69815c..7d4f529e0 100644 --- a/Model/lib/wdk/model/records/transcriptAttributeQueries.xml +++ b/Model/lib/wdk/model/records/transcriptAttributeQueries.xml @@ -1877,7 +1877,7 @@ LEFT JOIN ( WHERE ps.study_name = 'T.brucei paired end RNA Seq data from Horn [htseq-union - unstranded - tpm - unique]' AND ps.profile_type = 'values' - AND ta.org_abbrev IN (%%PARTITION_KEYS) + AND ta.org_abbrev IN (%%PARTITION_KEYS%%) GROUP BY ta.gene_source_id ) res ON ta.gene_source_id = res.gene_id From 9db34bd5f17bc6b4b2d88bf5a0833b642ee147ab Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Thu, 8 Jan 2026 12:23:32 -0500 Subject: [PATCH 61/66] speed up go enrich --- Model/lib/wdk/model/stepAnalysisParams.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Model/lib/wdk/model/stepAnalysisParams.xml b/Model/lib/wdk/model/stepAnalysisParams.xml index 6aa9357ef..cdfc154ac 100644 --- a/Model/lib/wdk/model/stepAnalysisParams.xml +++ b/Model/lib/wdk/model/stepAnalysisParams.xml @@ -224,7 +224,7 @@ The ontologies are three structured, controlled vocabularies that describe gene select organism as term, organism as display, organism as internal from (SELECT distinct ga.organism -FROM webready.GeneAttributes_p ga, +FROM apidbtuning.GeneAttributes ga, ($$answerIdSql$$) r where ga.source_id = r.gene_source_id and ga.gene_type in ('protein coding gene','pseudogene') @@ -243,7 +243,7 @@ order by ga.organism asc) q select ontology as term, ontology as display, ontology as internal from ( select distinct gts.ontology - from webready.GoTermSummary_p gts, + from apidbtuning.GoTermSummary gts, ($$answerIdSql$$) r where gts.gene_source_id = r.gene_source_id and gts.ontology is not null From de6dff7a41badf3b37bbc920ed0e35e0b82c8d83 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Thu, 8 Jan 2026 12:28:36 -0500 Subject: [PATCH 62/66] add GoTermSummary TT and speed some TTs --- .../xml/tuningManager/apiTuningManager.xml | 37 +++++++++++++++++-- 1 file changed, 33 insertions(+), 4 deletions(-) diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml index b850e6dcd..fd14f9c1b 100644 --- a/Model/lib/xml/tuningManager/apiTuningManager.xml +++ b/Model/lib/xml/tuningManager/apiTuningManager.xml @@ -93,6 +93,33 @@ + + + + + + + + + + + + + + + + + @@ -283,6 +310,7 @@ The trick sql was cribbed and modified from: nuijten.blogspot.com/2011/08/splitting-comma-delimited-string-regexp.html --> + @@ -969,7 +997,7 @@ create index Organism_projectId_idx&1 ON OrganismAttributes&1 (project_id, sourc - + - + + From 5304936efa7238498b153cc5d8a096a75545ba76 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Thu, 8 Jan 2026 16:27:22 -0500 Subject: [PATCH 63/66] fix pathway search default --- Model/lib/wdk/model/questions/params/pathwayParams.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Model/lib/wdk/model/questions/params/pathwayParams.xml b/Model/lib/wdk/model/questions/params/pathwayParams.xml index ff2b4d3c3..a4e4971bf 100644 --- a/Model/lib/wdk/model/questions/params/pathwayParams.xml +++ b/Model/lib/wdk/model/questions/params/pathwayParams.xml @@ -58,7 +58,7 @@ prompt="Pathway Source" quote="true"> Use only pathways from the selected source in this query. - + Date: Thu, 8 Jan 2026 20:58:00 -0500 Subject: [PATCH 64/66] fix Horn pheno query --- Model/lib/wdk/model/questions/params/geneParams.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Model/lib/wdk/model/questions/params/geneParams.xml b/Model/lib/wdk/model/questions/params/geneParams.xml index f2c1c0c74..1554954aa 100644 --- a/Model/lib/wdk/model/questions/params/geneParams.xml +++ b/Model/lib/wdk/model/questions/params/geneParams.xml @@ -8021,8 +8021,8 @@ products of your selected type (or types).

end as display FROM apidbtuning.profiletype WHERE profile_set_name in ( - 'T.brucei paired end RNA Seq data from Horn aligned with cds coordinates [htseq-union - unstranded - tpm - unique]', - 'T.brucei paired end RNA Seq data from Horn [htseq-union - unstranded - tpm - unique]' + 'T.brucei paired end RNA Seq data from Horn aligned with cds coordinates', + 'T.brucei paired end RNA Seq data from Horn' ) AND profile_type = 'values' ORDER BY term desc From 6e76a2c8b21c2443f8fdf133765a6465941337a5 Mon Sep 17 00:00:00 2001 From: bindu Date: Fri, 9 Jan 2026 15:24:14 -0500 Subject: [PATCH 65/66] fix a couple of queries needed for graphs --- Model/lib/xml/dataPlotter/queries.xml | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/Model/lib/xml/dataPlotter/queries.xml b/Model/lib/xml/dataPlotter/queries.xml index fae593b61..080037f3b 100644 --- a/Model/lib/xml/dataPlotter/queries.xml +++ b/Model/lib/xml/dataPlotter/queries.xml @@ -16,7 +16,7 @@ (select * from apidbTuning.DatasetProperty where property = 'switchStrandsProfiles') dprop, - (select '' as dataset_name, 1 as order_num from dual + (select '' as dataset_name, 1 as order_num -- TEMPLATE_ANCHOR transcriptionSummaryGraph ) ds where p.dataset_type = 'transcript_expression' @@ -62,7 +62,6 @@ where dd.dataset_presenter_id = '$datasetPresenterId' and pt.dataset_name = dd.name and pt.profile_study_id = dr.node_set_id - --and dr.study_id is null ]]> @@ -73,14 +72,13 @@ from apidbtuning.profile p , apidbtuning.Datasetdatasource dd , apidbtuning.profiletype pt - LEFT JOIN (select distinct sl.study_id - from study.studylink sl, apidbtuning.PanResults panr + LEFT JOIN (select distinct sl.node_set_id + from study.nodeNodeSet sl, apidbtuning.PanResults panr where sl.protocol_app_node_id = panr.pan_id and panr.result_table = - 'Results::NAFeatureDiffResult') dr ON pt.profile_study_id = dr.study_id + 'Results::NAFeatureDiffResult') dr ON pt.profile_study_id = dr.node_set_id where dd.dataset_presenter_id = '$datasetPresenterId' and pt.dataset_name = dd.name - and dr.study_id is null and p.profile_study_id = pt.profile_study_id and p.profile_type = pt.profile_type and p.source_id = '$sourceId' From d6589d870bb67db8ea9ee3e5c3e0e0a678f110d8 Mon Sep 17 00:00:00 2001 From: bindu Date: Mon, 12 Jan 2026 12:43:31 -0500 Subject: [PATCH 66/66] fix profile_set query --- Model/lib/xml/dataPlotter/queries.xml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/Model/lib/xml/dataPlotter/queries.xml b/Model/lib/xml/dataPlotter/queries.xml index 080037f3b..9ef1c8568 100644 --- a/Model/lib/xml/dataPlotter/queries.xml +++ b/Model/lib/xml/dataPlotter/queries.xml @@ -123,8 +123,7 @@ from (select row_number() OVER () as rn, points.* from ( , profile_type, node_type , node_order_num, dataset_name, study_id as profile_study_id FROM apidbtuning.ProfileSamples - WHERE node_type like 'htseq-union%' - AND profile_type = 'values' + WHERE profile_type = 'values' AND study_name = '$profileSetName' ORDER BY node_order_num) points )pts, @@ -134,7 +133,6 @@ from (select row_number() OVER () as rn, points.* from ( FROM apidbtuning.Profile p where p.profile_type = 'values' AND p.profile_set_name = '$profileSetName' - and p.node_type like 'htseq-union%' ) vs ) vals where pts.rn = vals.rn