From 1447c9ff12a2595a3803b61f1457e94039c392d4 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Thu, 24 Jul 2025 14:11:49 -0400 Subject: [PATCH 01/10] use category= in links file --- Model/config/datasetLinks.xml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/Model/config/datasetLinks.xml b/Model/config/datasetLinks.xml index e5c6804947..f658be0acd 100644 --- a/Model/config/datasetLinks.xml +++ b/Model/config/datasetLinks.xml @@ -1,6 +1,6 @@ - + View the DEFAULT_PROJECT Genomic Sequence Page for an Example Sequence - + View a partial region of an Example Sequence in the DEFAULT_PROJECT Genome Browser - + View the DEFAULT_PROJECT Organism Record Page - + Download Genome Data from DEFAULT_PROJECT - + Run BLAST on sequences in DEFAULT_PROJECT + Run BLAST on sequences in DEFAULT_PROJECT Date: Mon, 4 Aug 2025 18:36:44 -0400 Subject: [PATCH 02/10] fix categories --- Model/config/datasetLinks.xml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/Model/config/datasetLinks.xml b/Model/config/datasetLinks.xml index f658be0acd..66a6a6305b 100644 --- a/Model/config/datasetLinks.xml +++ b/Model/config/datasetLinks.xml @@ -62,7 +62,7 @@ Go to download directory for Current Relase of this particular organism. - + View peptides aligned to an Example Protein in the DEFAULT_PROJECT Genome Browser + View peptides aligned to an Example Protein in the DEFAULT_PROJECT Protein Browser - + View the DEFAULT_PROJECT Proteomics Section on an Example Gene Page - + View All Quantitative Proteomics Searches at DEFAULT_PROJECT @@ -101,7 +101,7 @@ Go to download directory for Current Relase of this particular organism. - + View All Microarray Searches at DEFAULT_PROJECT - + View All RNA-Seq Searches at DEFAULT_PROJECT - + View/Download this Data Set in the DEFAULT_PROJECT Genome Browser - + View/Download this Data Set in the DEFAULT_PROJECT Genome Browser Date: Thu, 21 Aug 2025 11:54:06 -0400 Subject: [PATCH 03/10] datasetdatasource table --- Model/bin/jbrowseOrganismList | 6 +-- Model/lib/dst/profileGraphs.dst | 20 ++++----- Model/lib/perl/JbrowseRnaSeqJunctionTracks.pm | 2 +- .../model/questions/params/datasetParams.xml | 6 +-- .../wdk/model/questions/params/geneParams.xml | 30 ++++++------- .../model/questions/params/sharedParams.xml | 10 ++--- .../model/records/geneAttributeQueries.xml | 10 ++--- .../wdk/model/records/geneTableQueries.xml | 28 ++++++------ .../model/records/genomicAttributeQueries.xml | 16 +++---- .../records/organismAttributeQueries.xml | 44 +++++++++---------- .../model/records/organismTableQueries.xml | 12 ++--- .../records/transcriptAttributeQueries.xml | 20 ++++----- Model/lib/xml/dataPlotter/queries.xml | 12 ++--- Model/lib/xml/jbrowse/genomeQueries.xml | 6 +-- 14 files changed, 111 insertions(+), 111 deletions(-) diff --git a/Model/bin/jbrowseOrganismList b/Model/bin/jbrowseOrganismList index 1644fc0d8a..9c64e4fc31 100644 --- a/Model/bin/jbrowseOrganismList +++ b/Model/bin/jbrowseOrganismList @@ -29,9 +29,9 @@ and ts.taxon_id = o.taxon_id "; my $historySql = "select h.build_number, o.public_abbrev, h.genome_source, h.genome_version, h.annotation_source, h.annotation_version - from apidbtuning.datasethistory h, apidbtuning.datasetnametaxon nt, apidb.organism o - where h.dataset_presenter_id = nt.dataset_presenter_id - and nt.name like '%primary_genome_RSRC' + from apidbtuning.datasethistory h, apidbtuning.datasetdatasource dd, apidb.organism o + where h.dataset_presenter_id = dd.dataset_presenter_id + and dd.name like '%primary_genome_RSRC' and h.annotation_version is not null and o.taxon_id = nt.taxon_id"; diff --git a/Model/lib/dst/profileGraphs.dst b/Model/lib/dst/profileGraphs.dst index 675147a2d3..dd728ef866 100644 --- a/Model/lib/dst/profileGraphs.dst +++ b/Model/lib/dst/profileGraphs.dst @@ -224,16 +224,16 @@ prop=includeProjectsExcludeEuPathDB , APIDBTUNING.DATASETPROPERTY dp , APIDBTUNING.DATASETPROPERTY dp2 , APIDBTUNING.DATASETPROPERTY dp3 - , APIDBTUNING.datasetnametaxon dnt + , APIDBTUNING.datasetdatasource dd where ps.DATASET_NAME = '${datasetName}' and ps.profile_type = 'values' and ps.dataset_name = ct.dataset_name - and ps.dataset_name = dnt.name - and dnt.dataset_presenter_id = dp.dataset_presenter_id + and ps.dataset_name = dd.name + and dd.dataset_presenter_id = dp.dataset_presenter_id and dp.property = 'profileSamplesHelp' - and dnt.dataset_presenter_id = dp2.dataset_presenter_id + and dd.dataset_presenter_id = dp2.dataset_presenter_id and dp2.property = 'datasetShortDisplayName' - and dnt.dataset_presenter_id = dp3.dataset_presenter_id + and dd.dataset_presenter_id = dp3.dataset_presenter_id and dp3.property = 'datasetDisplayName' ORDER BY ps.study_id, ps.NODE_ORDER_NUM ]]> @@ -324,15 +324,15 @@ FROM apidbtuning.profilesamples ps , APIDBTUNING.DATASETPROPERTY dp , APIDBTUNING.DATASETPROPERTY dp2 , APIDBTUNING.DATASETPROPERTY dp3 - , APIDBTUNING.datasetnametaxon dnt + , APIDBTUNING.datasetdatasource dd WHERE ps.DATASET_NAME = '${datasetName}' AND ps.profile_type = 'values' -and ps.dataset_name = dnt.name -and dnt.dataset_presenter_id = dp.dataset_presenter_id +and ps.dataset_name = dd.name +and dd.dataset_presenter_id = dp.dataset_presenter_id and dp.property = 'profileSamplesHelp' -and dnt.dataset_presenter_id = dp2.dataset_presenter_id +and dd.dataset_presenter_id = dp2.dataset_presenter_id and dp2.property = 'datasetShortDisplayName' -and dnt.dataset_presenter_id = dp3.dataset_presenter_id +and dd.dataset_presenter_id = dp3.dataset_presenter_id and dp3.property = 'datasetDisplayName' ORDER BY ps.study_id, ps.NODE_ORDER_NUM ]]> diff --git a/Model/lib/perl/JbrowseRnaSeqJunctionTracks.pm b/Model/lib/perl/JbrowseRnaSeqJunctionTracks.pm index 0a68c6884a..41cfb2a6b0 100644 --- a/Model/lib/perl/JbrowseRnaSeqJunctionTracks.pm +++ b/Model/lib/perl/JbrowseRnaSeqJunctionTracks.pm @@ -50,7 +50,7 @@ sub processOrganism { my $sql = "select count(*) from apidbtuning.datasetproperty p - , apidbtuning.datasetnametaxon d + , apidbtuning.datasetdatasource d , apidb.organism o where d.DATASET_PRESENTER_ID = p.DATASET_PRESENTER_ID and o.taxon_id = d.taxon_id diff --git a/Model/lib/wdk/model/questions/params/datasetParams.xml b/Model/lib/wdk/model/questions/params/datasetParams.xml index 4617b42725..ce95bc7f9c 100644 --- a/Model/lib/wdk/model/questions/params/datasetParams.xml +++ b/Model/lib/wdk/model/questions/params/datasetParams.xml @@ -117,8 +117,8 @@ @@ -145,7 +145,7 @@ select 'any', -1 diff --git a/Model/lib/wdk/model/questions/params/geneParams.xml b/Model/lib/wdk/model/questions/params/geneParams.xml index b652d5ec27..a8fe825204 100644 --- a/Model/lib/wdk/model/questions/params/geneParams.xml +++ b/Model/lib/wdk/model/questions/params/geneParams.xml @@ -6422,10 +6422,10 @@ products of your selected type (or types).

select distinct 'long_transcript_novelty' as ontology_term_name, cast(null as varchar(1)) as parent_ontology_term_name, 'Support From Long Read Evidence' as display_name, 'Find genes based on overlapping models from long read RNA sequencing, for example from Oxford Nanopore or PacBio sequencing platforms. To be considered in this query, a model must have at least 5 supporting reads and be at least 20 bases long. Categories as follows: Novel in Collection (NIC): Prediction uses known splice donors and acceptors but reveals new connections (e.g., skipped exon isoforms); Incomplete Splice Match (ISM): Prediction matches subsection of a known transcript model, but has a novel putative start or end point; Novel Not In Collection (NNC): Prediction has at least one novel splice donor or acceptor; Genomic: Prediction has no overlapping splice junctions compared to known transcripts; Genomic: Prediction has no overlapping splice junctions compared to known transcripts; Known: Prediction exactly matches a known model. NOTE: The percentage add up to more than 100% because one existing gene model can have more than associated TALON model.' as description, cast(null as varchar(1)) as units, 'string' as type, 0 as is_range, cast(null as varchar(1)) as precision, 7 as display_order - from apidbtuning.datasetnametaxon dnt + from apidbtuning.datasetdatasource dd where '$$gene_or_transcript$$' = 'gene_source_id' - and dnt.name like '%nanopore_rnaSeqNextflow_RSRC' - and dnt.taxon_id in ($$organism_select_all$$) + and dd.name like '%nanopore_rnaSeqNextflow_RSRC' + and dd.taxon_id in ($$organism_select_all$$) and '@PROJECT_ID@' != 'EuPathDB' UNION select 'intron_junction' as ontology_term_name, cast(null as varchar(1)) as parent_ontology_term_name, @@ -6608,8 +6608,8 @@ products of your selected type (or types).

FROM sres.externaldatabaserelease edr , sres.externaldatabase ed , apidbtuning.datasetpresenter dsp - , apidbtuning.datasetnametaxon dnt - WHERE dnt.taxon_id = $$organismsWithSingleCell$$ + , apidbtuning.datasetdatasource dd + WHERE dd.taxon_id = $$organismsWithSingleCell$$ AND dsp.name like '%cellxgene%' AND dsp.name = dnt.name AND ed.name = dnt.name @@ -8869,7 +8869,7 @@ end as term sdi.sort_order FROM apidbTuning.sampledisplayinfo sdi, apidbTuning.datasetPresenter dsp, - apidbTuning.datasetNameTaxon dsnt, + apidbTuning.datasetdatasource dd, apidbTuning.datasetContact dsc, (SELECT DISTINCT ta.organism,ta.taxon_id,ta.project_id FROM apidbtuning.transcriptattributes ta, apidb.massspecpeptide msf @@ -8877,11 +8877,11 @@ end as term and (ta.project_id = '@PROJECT_ID@' OR 'UniDB' = '@PROJECT_ID@') ) org WHERE sdi.dataset_name like '%_massSpec_%' - AND sdi.dataset_name = dsnt.name - AND dsc.dataset_presenter_id = dsnt.dataset_presenter_id - AND dsp.dataset_presenter_id = dsnt.dataset_presenter_id + AND sdi.dataset_name = dd.name + AND dsc.dataset_presenter_id = dd.dataset_presenter_id + AND dsp.dataset_presenter_id = dd.dataset_presenter_id AND Dsc.Is_Primary_Contact = true - AND dsnt.taxon_id = org.taxon_id + AND dd.taxon_id = org.taxon_id ) SELECT replace(replace(term,',',''),(''''), '') as term, replace(replace(parentTerm,',', ''),(''''), '') as parentTerm, @@ -10164,16 +10164,16 @@ end as term diff --git a/Model/lib/wdk/model/questions/params/sharedParams.xml b/Model/lib/wdk/model/questions/params/sharedParams.xml index 0f48be89e5..0e017b165d 100644 --- a/Model/lib/wdk/model/questions/params/sharedParams.xml +++ b/Model/lib/wdk/model/questions/params/sharedParams.xml @@ -3074,19 +3074,19 @@ This parameter allows you to apply the minimum number of peptides to each select diff --git a/Model/lib/wdk/model/records/geneAttributeQueries.xml b/Model/lib/wdk/model/records/geneAttributeQueries.xml index 3d69efb4c8..ab100f8b9d 100644 --- a/Model/lib/wdk/model/records/geneAttributeQueries.xml +++ b/Model/lib/wdk/model/records/geneAttributeQueries.xml @@ -604,20 +604,20 @@ GROUP BY source_id SELECT ga.source_id, ga.project_id, v.annotation_version as ds_annotation_version, v.dataset_presenter_id as dataset_id, v.description as attribution_partial FROM apidbtuning.geneattributes ga LEFT JOIN ( - SELECT ga.source_id, ga.project_id,dsh.annotation_version,dsh.annotation_source, dnt.dataset_presenter_id, dsp.description + SELECT ga.source_id, ga.project_id,dsh.annotation_version,dsh.annotation_source, dd.dataset_presenter_id, dsp.description FROM ( SELECT max(dsh.build_number) bld, dsh.dataset_presenter_id FROM apidbtuning.datasethistory dsh WHERE dsh.annotation_version is not null GROUP BY dsh.dataset_presenter_id ) dpb - , apidbtuning.datasethistory dsh, apidbtuning.datasetnametaxon dnt + , apidbtuning.datasethistory dsh, apidbtuning.datasetsource dd , apidbtuning.geneattributes ga, apidbtuning.datasetpresenter dsp WHERE dpb.bld = dsh.BUILD_NUMBER AND dpb.dataset_presenter_id = dsh.DATASET_PRESENTER_ID - AND dnt.dataset_presenter_id = dsp.dataset_presenter_id - AND dsh.dataset_presenter_id = dnt.dataset_presenter_id - AND dnt.taxon_id = ga.taxon_id + AND dd.dataset_presenter_id = dsp.dataset_presenter_id + AND dsh.dataset_presenter_id = dd.dataset_presenter_id + AND dd.taxon_id = ga.taxon_id ) v ON ga.source_id = v.source_id AND ga.project_id = v.project_id ]]> diff --git a/Model/lib/wdk/model/records/geneTableQueries.xml b/Model/lib/wdk/model/records/geneTableQueries.xml index bcdf99863c..1f8e437b93 100644 --- a/Model/lib/wdk/model/records/geneTableQueries.xml +++ b/Model/lib/wdk/model/records/geneTableQueries.xml @@ -4269,7 +4269,7 @@ from apidbTuning.AllGeneProducts , d.percentile_channel1 , d.percentile_channel2 , ga.project_id - FROM apidbTuning.ExpressionGraphsData d, apidbTuning.DatasetNameTaxon dp, + FROM apidbTuning.ExpressionGraphsData d, apidbTuning.DatasetDatasource dp, apidbTuning.GeneGroupProfile ggp, apidbtuning.geneattributes ga -- customisation for Hehl datasets WHERE ((dp.dataset_presenter_id = 'DS_173528b522' AND d.dataset_id IN ('DS_173528b522', 'DS_e7467c0306')) @@ -4326,7 +4326,7 @@ from apidbTuning.AllGeneProducts @@ -4518,7 +4518,7 @@ SELECT genes.string_value AS gene, ag.display_name AS variable, av.string_value, SELECT ggp.source_id , ggp.profile_graph_id AS gene , ga.project_id - , dnt.dataset_presenter_id AS dataset_id + , dd.dataset_presenter_id AS dataset_id , coalesce(psdi.profile_set_display_name, ps.name) AS profile_set_display_name , pan.name AS sample_name , CASE WHEN cp.score_type = 'mutability in CDS' @@ -4536,7 +4536,7 @@ SELECT genes.string_value AS gene, ag.display_name AS variable, av.string_value, , study.study i , sres.externaldatabaserelease r , sres.externaldatabase d - , apidbtuning.datasetnametaxon dnt + , apidbtuning.datasetsource dd , apidbtuning.profile p , apidbtuning.geneGroupProfile ggp WHERE ga.na_feature_id = cp.na_feature_id @@ -4548,7 +4548,7 @@ SELECT genes.string_value AS gene, ag.display_name AS variable, av.string_value, AND ps.investigation_id = i.study_id AND i.external_database_release_id = r.external_database_release_id AND r.external_database_id = d.external_database_id - AND d.name = dnt.name + AND d.name = dd.name AND ggp.profile_graph_id = ga.source_id AND d.name in ('pfal3D7_phenotype_pB_mutagenesis_MIS_MFS_RSRC', 'pknoH_phenotype_piggyBac_mutagenesis_HME_MIS_OIS_RSRC', @@ -4557,7 +4557,7 @@ SELECT genes.string_value AS gene, ag.display_name AS variable, av.string_value, SELECT ggp.source_id , ggp.profile_graph_id AS gene , ga.project_id - , dnt.dataset_presenter_id AS dataset_id + , dd.dataset_presenter_id AS dataset_id , coalesce(psdi.profile_set_display_name, ps.name) AS profile_set_display_name , pan.name AS sample_name , round(cp.relative_growth_rate, 2)::VARCHAR AS phenotype_score @@ -4572,7 +4572,7 @@ SELECT genes.string_value AS gene, ag.display_name AS variable, av.string_value, , study.study i , sres.externaldatabaserelease r , sres.externaldatabase d - , apidbtuning.datasetnametaxon dnt + , apidbtuning.datasetsource dd , apidbtuning.profile p , apidbtuning.geneGroupProfile ggp WHERE ga.na_feature_id = cp.na_feature_id @@ -4584,7 +4584,7 @@ SELECT genes.string_value AS gene, ag.display_name AS variable, av.string_value, AND ps.investigation_id = i.study_id AND i.external_database_release_id = r.external_database_release_id AND r.external_database_id = d.external_database_id - AND d.name = dnt.name + AND d.name = dd.name AND ggp.profile_graph_id = ga.source_id ]]> diff --git a/Model/lib/wdk/model/records/genomicAttributeQueries.xml b/Model/lib/wdk/model/records/genomicAttributeQueries.xml index 203d5e425c..fb90d983ef 100644 --- a/Model/lib/wdk/model/records/genomicAttributeQueries.xml +++ b/Model/lib/wdk/model/records/genomicAttributeQueries.xml @@ -268,14 +268,14 @@ CASE WHEN (p.dataset_presenter_id in (SELECT dataset_presenter_id FROM apidbtuning.datasetpublication WHERE pmid IS NOT NULL ) ) THEN 1 ELSE 0 END AS is_annotated - FROM APIDBTUNING.datasetnametaxon dt, + FROM APIDBTUNING.datasetdatasource dd, ApidbTuning.GenomicSeqAttributes sa, apidb.datasource ds, apidbtuning.datasetpresenter p - WHERE sa.taxon_id = dt.taxon_id - AND dt.name = ds.name + WHERE sa.taxon_id = dd.taxon_id + AND dd.name = ds.name AND ds.type = 'genome' - AND dt.dataset_presenter_id = p.dataset_presenter_id + AND dd.dataset_presenter_id = p.dataset_presenter_id ]]> @@ -295,10 +295,10 @@ , '' || dp.display_name || '
' as dataset_page FROM apidbtuning.genomicseqattributes gs , apidbtuning.datasetpresenter dp - , apidbtuning.datasetnametaxon dnt - WHERE gs.taxon_id = dnt.taxon_id - and dnt.name like '%_primary_genome_RSRC' - and dnt.dataset_presenter_id = dp.dataset_presenter_id + , apidbtuning.datasetsource dd + WHERE gs.taxon_id = dd.taxon_id + and dd.name like '%_primary_genome_RSRC' + and dd.dataset_presenter_id = dp.dataset_presenter_id ]]> diff --git a/Model/lib/wdk/model/records/organismAttributeQueries.xml b/Model/lib/wdk/model/records/organismAttributeQueries.xml index 170cf68668..6abd01d66b 100644 --- a/Model/lib/wdk/model/records/organismAttributeQueries.xml +++ b/Model/lib/wdk/model/records/organismAttributeQueries.xml @@ -200,12 +200,12 @@ GROUP BY dsh.dataset_presenter_id ) dpb , apidbtuning.datasethistory dsh - , apidbtuning.datasetnametaxon dnt + , apidbtuning.datasetdatasource dd , apidbtuning.organismattributes oa WHERE dpb.bld = dsh.BUILD_NUMBER AND dpb.dataset_presenter_id = dsh.DATASET_PRESENTER_ID - AND dsh.dataset_presenter_id = dnt.dataset_presenter_id - AND dnt.name like oa.internal_abbrev || '\_primary_genome%' escape '\' + AND dsh.dataset_presenter_id = dd.dataset_presenter_id + AND dd.name like oa.internal_abbrev || '\_primary_genome%' escape '\' ) v ON oa.source_id = v.source_id AND oa.project_id = v.project_id ]]> @@ -228,12 +228,12 @@ WHERE dsh.genome_version is not null GROUP BY dsh.dataset_presenter_id ) dpb - , apidbtuning.datasethistory dsh, apidbtuning.datasetnametaxon dnt + , apidbtuning.datasethistory dsh, apidbtuning.datasetdatasource dd , apidbtuning.organismattributes oa WHERE dpb.bld = dsh.BUILD_NUMBER AND dpb.dataset_presenter_id = dsh.DATASET_PRESENTER_ID - AND dsh.dataset_presenter_id = dnt.dataset_presenter_id - AND dnt.name like oa.internal_abbrev || '\_primary_genome%' escape '\' + AND dsh.dataset_presenter_id = dd.dataset_presenter_id + AND dd.name like oa.internal_abbrev || '\_primary_genome%' escape '\' ) v ON oa.source_id = v.source_id AND oa.project_id = v.project_id ]]> @@ -324,14 +324,14 @@ FROM apidbtuning.organismattributes o (SELECT dataset_presenter_id FROM apidbtuning.datasetpublication WHERE pmid IS NOT NULL ) ) THEN 1 ELSE 0 END AS is_published , '' || dp.display_name || '
' as dataset_page - FROM APIDBTUNING.datasetnametaxon dt, + FROM APIDBTUNING.datasedatasource dd, apidbtuning.organismattributes o, apidb.datasource ds, apidbtuning.datasetpresenter dp - WHERE o.component_taxon_id = dt.taxon_id - AND dt.name = ds.name + WHERE o.component_taxon_id = dd.taxon_id + AND dd.name = ds.name AND ds.type = 'genome' - AND dt.dataset_presenter_id = dp.dataset_presenter_id + AND dd.dataset_presenter_id = dp.dataset_presenter_id ]]> @@ -344,14 +344,14 @@ FROM apidbtuning.organismattributes o @@ -366,7 +366,7 @@ FROM apidbtuning.organismattributes o @@ -385,7 +385,7 @@ FROM apidbtuning.organismattributes o diff --git a/Model/lib/wdk/model/records/organismTableQueries.xml b/Model/lib/wdk/model/records/organismTableQueries.xml index bfb9b1682a..8a605d8e2e 100644 --- a/Model/lib/wdk/model/records/organismTableQueries.xml +++ b/Model/lib/wdk/model/records/organismTableQueries.xml @@ -51,10 +51,10 @@ order by source_id, count(*) desc @@ -62,11 +62,11 @@ order by source_id, count(*) desc diff --git a/Model/lib/wdk/model/records/transcriptAttributeQueries.xml b/Model/lib/wdk/model/records/transcriptAttributeQueries.xml index 594f09496b..6df2933175 100644 --- a/Model/lib/wdk/model/records/transcriptAttributeQueries.xml +++ b/Model/lib/wdk/model/records/transcriptAttributeQueries.xml @@ -922,8 +922,8 @@ ELSE 'N/A' end as apollo_link_out coalesce(string_agg(ta.target_name, ', ' order by ta.target_name), '0') as tablesForOrg FROM ( SELECT distinct dmr.target_name, tn.name - FROM ApidbTuning.DatasetNameTaxon dt - INNER JOIN ApidbTuning.DatasetModelRef dmr ON dt.dataset_presenter_id = dmr.dataset_presenter_id + FROM ApidbTuning.DatasetDatasource dd + INNER JOIN ApidbTuning.DatasetModelRef dmr ON dd.dataset_presenter_id = dmr.dataset_presenter_id LEFT JOIN sres.TaxonName tn dt.taxon_id = tn.taxon_id WHERE AND dmr.target_type = 'table' @@ -1125,14 +1125,14 @@ ELSE 'N/A' end as apollo_link_out SELECT dataset_presenter_id FROM apidbtuning.datasetpublication WHERE pmid IS NOT NULL ) ) THEN 1 ELSE 0 END AS is_annotated - FROM APIDBTUNING.datasetnametaxon dt, + FROM APIDBTUNING.datasetdatasource dd, apidbtuning.geneattributes ga, apidb.datasource ds, apidbtuning.datasetpresenter p - WHERE ga.taxon_id = dt.taxon_id - AND dt.name = ds.name + WHERE ga.taxon_id = dd.taxon_id + AND dd.name = ds.name AND ds.type = 'genome' - AND dt.dataset_presenter_id = p.dataset_presenter_id + AND dd.dataset_presenter_id = p.dataset_presenter_id ]]> @@ -1146,14 +1146,14 @@ ELSE 'N/A' end as apollo_link_out diff --git a/Model/lib/xml/dataPlotter/queries.xml b/Model/lib/xml/dataPlotter/queries.xml index 9a38cffecc..a88b8b9741 100644 --- a/Model/lib/xml/dataPlotter/queries.xml +++ b/Model/lib/xml/dataPlotter/queries.xml @@ -56,9 +56,9 @@ where sl.protocol_app_node_id = panr.pan_id and panr.result_table = 'Results::NAFeatureExpression') dr - , apidbtuning.DatasetNameTaxon dnt - where dnt.dataset_presenter_id = '$datasetPresenterId' - and pt.dataset_name = dnt.name + , apidbtuning.Datasetdatasource dd + where dd.dataset_presenter_id = '$datasetPresenterId' + and pt.dataset_name = dd.name and pt.profile_study_id = dr.node_set_id --and dr.study_id is null ]]> @@ -74,9 +74,9 @@ where sl.protocol_app_node_id = panr.pan_id and panr.result_table = 'Results::NAFeatureDiffResult') dr - , apidbtuning.DatasetNameTaxon dnt - where dnt.dataset_presenter_id = '$datasetPresenterId' - and pt.dataset_name = dnt.name + , apidbtuning.Datasetdatasource dd + where dd.dataset_presenter_id = '$datasetPresenterId' + and pt.dataset_name = dd.name and pt.profile_study_id = dr.study_id (+) and dr.study_id is null and p.profile_study_id = pt.profile_study_id diff --git a/Model/lib/xml/jbrowse/genomeQueries.xml b/Model/lib/xml/jbrowse/genomeQueries.xml index dd9aef1bf7..393e7bd8a4 100644 --- a/Model/lib/xml/jbrowse/genomeQueries.xml +++ b/Model/lib/xml/jbrowse/genomeQueries.xml @@ -1269,7 +1269,7 @@ from dots.massspecfeature msf , APIDB.MASSSPECSUMMARY mss , study.protocolappnode pan , apidbtuning.sampledisplayinfo sdi - , apidbtuning.datasetnametaxon dnt + , apidbtuning.datasetdatasource dd , apidbtuning.datasetpresenter dsp , dots.aasequence aaseq , dots.aalocation aaloc @@ -1283,8 +1283,8 @@ and msf.MASS_SPEC_SUMMARY_ID = mss.MASS_SPEC_SUMMARY_ID and d.name = sdi.DATASET_NAME and mss.PROTOCOL_APP_NODE_ID = pan.PROTOCOL_APP_NODE_ID and (pan.name in (sdi.sample, sdi.sample || ' (MS Summary)') or sdi.sample is null) -and d.name = dnt.NAME -and dnt.DATASET_PRESENTER_ID = dsp.DATASET_PRESENTER_ID +and d.name = dd.NAME +and dd.DATASET_PRESENTER_ID = dsp.DATASET_PRESENTER_ID and msf.AA_SEQUENCE_ID = aaseq.aa_sequence_id and msf.AA_FEATURE_ID = aaloc.aa_feature_id ) From e532654695e4a65216e6399892db1676c3cbe080 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Thu, 21 Aug 2025 16:09:51 -0400 Subject: [PATCH 04/10] datasetproperty table --- Model/lib/dst/profileGraphs.dst | 4 ++-- Model/lib/xml/dataPlotter/queries.xml | 8 +++++--- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/Model/lib/dst/profileGraphs.dst b/Model/lib/dst/profileGraphs.dst index dd728ef866..7d41545320 100644 --- a/Model/lib/dst/profileGraphs.dst +++ b/Model/lib/dst/profileGraphs.dst @@ -229,7 +229,7 @@ prop=includeProjectsExcludeEuPathDB and ps.profile_type = 'values' and ps.dataset_name = ct.dataset_name and ps.dataset_name = dd.name - and dd.dataset_presenter_id = dp.dataset_presenter_id + and dd.name = dp.datasource_name and dp.property = 'profileSamplesHelp' and dd.dataset_presenter_id = dp2.dataset_presenter_id and dp2.property = 'datasetShortDisplayName' @@ -328,7 +328,7 @@ FROM apidbtuning.profilesamples ps WHERE ps.DATASET_NAME = '${datasetName}' AND ps.profile_type = 'values' and ps.dataset_name = dd.name -and dd.dataset_presenter_id = dp.dataset_presenter_id +and dd.name = dp.datasource_name and dp.property = 'profileSamplesHelp' and dd.dataset_presenter_id = dp2.dataset_presenter_id and dp2.property = 'datasetShortDisplayName' diff --git a/Model/lib/xml/dataPlotter/queries.xml b/Model/lib/xml/dataPlotter/queries.xml index a88b8b9741..382fb13fba 100644 --- a/Model/lib/xml/dataPlotter/queries.xml +++ b/Model/lib/xml/dataPlotter/queries.xml @@ -11,6 +11,7 @@ from apidbTuning.Profile p, apidbTuning.ProfileSamples ps, study.ProtocolAppNode pan, + apidbtuning.datasetdatasource dd, apidbTuning.DatasetPresenter dsp, (select * from apidbTuning.DatasetProperty @@ -30,9 +31,10 @@ and p.profile_set_name not like '%nonunique%' and p.profile_set_name = ps.study_name and ps.protocol_app_node_id = pan.protocol_app_node_id - and p.dataset_name = dsp.name - and dsp.name = ds.dataset_name - and dsp.dataset_presenter_id = dprop.dataset_presenter_id + and p.dataset_name = dd.name + and dd.name = ds.dataset_name + and dd.name = dprop.datasource_name + and dsp.dataset_presenter_id = dd.dataset_presenter_id order by ds.order_num ]]> From 73d5976ef5ff7ae19dbc872c7a33ced50adf11e0 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Wed, 27 Aug 2025 16:51:58 -0400 Subject: [PATCH 05/10] fix typos --- Model/lib/wdk/model/records/geneAttributeQueries.xml | 2 +- Model/lib/wdk/model/records/geneTableQueries.xml | 8 ++++---- Model/lib/wdk/model/records/genomicAttributeQueries.xml | 2 +- .../lib/wdk/model/records/transcriptAttributeQueries.xml | 2 +- 4 files changed, 7 insertions(+), 7 deletions(-) diff --git a/Model/lib/wdk/model/records/geneAttributeQueries.xml b/Model/lib/wdk/model/records/geneAttributeQueries.xml index ab100f8b9d..3c0975e316 100644 --- a/Model/lib/wdk/model/records/geneAttributeQueries.xml +++ b/Model/lib/wdk/model/records/geneAttributeQueries.xml @@ -611,7 +611,7 @@ GROUP BY source_id WHERE dsh.annotation_version is not null GROUP BY dsh.dataset_presenter_id ) dpb - , apidbtuning.datasethistory dsh, apidbtuning.datasetsource dd + , apidbtuning.datasethistory dsh, apidbtuning.datasetdatasource dd , apidbtuning.geneattributes ga, apidbtuning.datasetpresenter dsp WHERE dpb.bld = dsh.BUILD_NUMBER AND dpb.dataset_presenter_id = dsh.DATASET_PRESENTER_ID diff --git a/Model/lib/wdk/model/records/geneTableQueries.xml b/Model/lib/wdk/model/records/geneTableQueries.xml index 1f8e437b93..689c73382e 100644 --- a/Model/lib/wdk/model/records/geneTableQueries.xml +++ b/Model/lib/wdk/model/records/geneTableQueries.xml @@ -4341,7 +4341,7 @@ from apidbTuning.AllGeneProducts , study.study i , sres.externaldatabaserelease r , sres.externaldatabase d - , apidbtuning.datasetsource dd + , apidbtuning.datasetdatasource dd , apidbtuning.genegroupprofile ggp , apidbtuning.profilesamples smpl WHERE ga.na_feature_id = nfe.na_feature_id @@ -4448,7 +4448,7 @@ from apidbTuning.AllGeneProducts , study.study i , sres.externaldatabaserelease r , sres.externaldatabase d - , apidbtuning.datasetsource dd + , apidbtuning.datasetdatasource dd , apidbtuning.genegroupprofile ggp WHERE ga.na_feature_id = nfe.na_feature_id AND ggp.profile_graph_id = ga.source_id @@ -4536,7 +4536,7 @@ SELECT genes.string_value AS gene, ag.display_name AS variable, av.string_value, , study.study i , sres.externaldatabaserelease r , sres.externaldatabase d - , apidbtuning.datasetsource dd + , apidbtuning.datasetdatasource dd , apidbtuning.profile p , apidbtuning.geneGroupProfile ggp WHERE ga.na_feature_id = cp.na_feature_id @@ -4572,7 +4572,7 @@ SELECT genes.string_value AS gene, ag.display_name AS variable, av.string_value, , study.study i , sres.externaldatabaserelease r , sres.externaldatabase d - , apidbtuning.datasetsource dd + , apidbtuning.datasetdatasource dd , apidbtuning.profile p , apidbtuning.geneGroupProfile ggp WHERE ga.na_feature_id = cp.na_feature_id diff --git a/Model/lib/wdk/model/records/genomicAttributeQueries.xml b/Model/lib/wdk/model/records/genomicAttributeQueries.xml index fb90d983ef..60b145b6b2 100644 --- a/Model/lib/wdk/model/records/genomicAttributeQueries.xml +++ b/Model/lib/wdk/model/records/genomicAttributeQueries.xml @@ -295,7 +295,7 @@ , '' || dp.display_name || '
' as dataset_page FROM apidbtuning.genomicseqattributes gs , apidbtuning.datasetpresenter dp - , apidbtuning.datasetsource dd + , apidbtuning.datasetdatasource dd WHERE gs.taxon_id = dd.taxon_id and dd.name like '%_primary_genome_RSRC' and dd.dataset_presenter_id = dp.dataset_presenter_id diff --git a/Model/lib/wdk/model/records/transcriptAttributeQueries.xml b/Model/lib/wdk/model/records/transcriptAttributeQueries.xml index 6df2933175..7f051b6cc8 100644 --- a/Model/lib/wdk/model/records/transcriptAttributeQueries.xml +++ b/Model/lib/wdk/model/records/transcriptAttributeQueries.xml @@ -1146,7 +1146,7 @@ ELSE 'N/A' end as apollo_link_out Date: Wed, 27 Aug 2025 16:56:12 -0400 Subject: [PATCH 06/10] fix typos --- Model/lib/wdk/model/records/organismAttributeQueries.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Model/lib/wdk/model/records/organismAttributeQueries.xml b/Model/lib/wdk/model/records/organismAttributeQueries.xml index 6abd01d66b..d8f8d9c20e 100644 --- a/Model/lib/wdk/model/records/organismAttributeQueries.xml +++ b/Model/lib/wdk/model/records/organismAttributeQueries.xml @@ -324,7 +324,7 @@ FROM apidbtuning.organismattributes o (SELECT dataset_presenter_id FROM apidbtuning.datasetpublication WHERE pmid IS NOT NULL ) ) THEN 1 ELSE 0 END AS is_published , '' || dp.display_name || '
' as dataset_page - FROM APIDBTUNING.datasedatasource dd, + FROM APIDBTUNING.datasetdatasource dd, apidbtuning.organismattributes o, apidb.datasource ds, apidbtuning.datasetpresenter dp From 7f9f8f64365bd680fdfad30e7d894c9fccee49c8 Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Wed, 27 Aug 2025 20:42:51 -0400 Subject: [PATCH 07/10] fix category --- Model/lib/wdk/model/records/organismTableQueries.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Model/lib/wdk/model/records/organismTableQueries.xml b/Model/lib/wdk/model/records/organismTableQueries.xml index 8a605d8e2e..e61eff6158 100644 --- a/Model/lib/wdk/model/records/organismTableQueries.xml +++ b/Model/lib/wdk/model/records/organismTableQueries.xml @@ -52,7 +52,7 @@ order by source_id, count(*) desc @@ -64,7 +64,7 @@ order by source_id, count(*) desc select oa.source_id, oa.project_id, dsp.description from apidbtuning.datasetpresenter dsp, apidbtuning.datasetdatasource dd, APIDBTUNING.organismattributes oa, apidb.datasource ds - where dsp.type = 'genome' + where dd.category = 'Genome' and dsp.dataset_presenter_id = dd.dataset_presenter_id and dd.name = ds.name and oa.component_taxon_id = ds.taxon_id From d9e10625c750c0e24db9e712e7b9514061cd86d9 Mon Sep 17 00:00:00 2001 From: Steve <43149795+steve-fischer-200@users.noreply.github.com> Date: Fri, 29 Aug 2025 14:34:03 -0400 Subject: [PATCH 08/10] Update organismTableQueries.xml fix 'Genomes' --- Model/lib/wdk/model/records/organismTableQueries.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Model/lib/wdk/model/records/organismTableQueries.xml b/Model/lib/wdk/model/records/organismTableQueries.xml index e61eff6158..b7dd1b341f 100644 --- a/Model/lib/wdk/model/records/organismTableQueries.xml +++ b/Model/lib/wdk/model/records/organismTableQueries.xml @@ -64,7 +64,7 @@ order by source_id, count(*) desc select oa.source_id, oa.project_id, dsp.description from apidbtuning.datasetpresenter dsp, apidbtuning.datasetdatasource dd, APIDBTUNING.organismattributes oa, apidb.datasource ds - where dd.category = 'Genome' + where dd.category = 'Genomes' and dsp.dataset_presenter_id = dd.dataset_presenter_id and dd.name = ds.name and oa.component_taxon_id = ds.taxon_id From f55fae274e0877c19cb3a7c234c857948fef1fc8 Mon Sep 17 00:00:00 2001 From: Steve <43149795+steve-fischer-200@users.noreply.github.com> Date: Fri, 29 Aug 2025 14:36:03 -0400 Subject: [PATCH 09/10] Update organismTableQueries.xml fix 'Genomes' --- Model/lib/wdk/model/records/organismTableQueries.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Model/lib/wdk/model/records/organismTableQueries.xml b/Model/lib/wdk/model/records/organismTableQueries.xml index b7dd1b341f..12c2a98902 100644 --- a/Model/lib/wdk/model/records/organismTableQueries.xml +++ b/Model/lib/wdk/model/records/organismTableQueries.xml @@ -52,7 +52,7 @@ order by source_id, count(*) desc From 6bca97dfe6061c6d534db1bc608a10f2ea3194df Mon Sep 17 00:00:00 2001 From: steve-fischer-200 Date: Fri, 5 Sep 2025 11:37:35 -0400 Subject: [PATCH 10/10] use datasetdatasource in tuning mgr --- .../xml/tuningManager/apiTuningManager.xml | 38 +++++++++---------- 1 file changed, 19 insertions(+), 19 deletions(-) diff --git a/Model/lib/xml/tuningManager/apiTuningManager.xml b/Model/lib/xml/tuningManager/apiTuningManager.xml index 7e341f4a54..240197f9f2 100644 --- a/Model/lib/xml/tuningManager/apiTuningManager.xml +++ b/Model/lib/xml/tuningManager/apiTuningManager.xml @@ -6482,8 +6482,8 @@ delete from &prefixGeneProduct&1 where product is null INNER JOIN sres.externaldatabaserelease r ON msp.external_database_release_id = r.external_database_release_id INNER JOIN sres.externaldatabase d ON r.external_database_id = d.external_database_id LEFT JOIN transcriptattributes ga ON msp.protein_source_id = ga.protein_source_id - LEFT JOIN datasetnametaxon dsnt ON d.name = dsnt.name - LEFT JOIN datasetpresenter dsp ON dsnt.dataset_presenter_id = dsp.dataset_presenter_id + LEFT JOIN datasetdatasource dd ON d.name = dd.name + LEFT JOIN datasetpresenter dsp ON dd.dataset_presenter_id = dsp.dataset_presenter_id GROUP BY d.name, ga.source_id, ga.gene_source_id, ga.project_id, dsp.display_name, msp.protein_source_id, ga.aa_sequence_id, msp.peptide_sequence, msp.spectrum_count, msp.peptide_start, msp.peptide_end, msp.external_database_release_id, msp.sample @@ -6611,8 +6611,8 @@ delete from &prefixGeneProduct&1 where product is null INNER JOIN sres.externaldatabaserelease r ON msp.external_database_release_id = r.external_database_release_id INNER JOIN sres.externaldatabase d ON r.external_database_id = d.external_database_id LEFT JOIN transcriptattributes ga ON msp.protein_source_id = ga.protein_source_id - LEFT JOIN datasetnametaxon dsnt ON d.name = dsnt.name - LEFT JOIN datasetpresenter dsp ON dsnt.dataset_presenter_id = dsp.dataset_presenter_id + LEFT JOIN datasetdatasource dd ON d.name = dd.name + LEFT JOIN datasetpresenter dsp ON dd.dataset_presenter_id = dsp.dataset_presenter_id GROUP BY d.name, ga.source_id, ga.gene_source_id, ga.project_id, dsp.display_name, msp.protein_source_id, ga.aa_sequence_id, msp.peptide_sequence, msp.spectrum_count, msp.peptide_start, msp.peptide_end, msp.external_database_release_id, @@ -6736,12 +6736,12 @@ delete from &prefixGeneProduct&1 where product is null from GenomicSeqAttributes sa where sa.is_top_level = 1 ), macros as ( - SELECT dnt.dataset_presenter_id + SELECT dd.dataset_presenter_id , o.name_for_filenames , o.project_id , o.public_abbrev as org_abbrev , o.source_id as org_pk - , dnt.name + , dd.name , dsp.name as dataset_presenter_name , sa.source_id as sequence_source_id , pg.sequence_id as p_sequence_source_id @@ -6750,11 +6750,11 @@ delete from &prefixGeneProduct&1 where product is null , rg.sequence_id as r_sequence_source_id , rg.gene_source_id as r_gene_id FROM organismattributes o - INNER JOIN datasetnametaxon dnt ON o.component_taxon_id = dnt.taxon_id - INNER JOIN datasetpresenter dsp ON dnt.dataset_presenter_id = dsp.dataset_presenter_id - INNER JOIN sequences sa ON dnt.taxon_id = sa.taxon_id - LEFT JOIN (select * from proteomicsgenes where rn = 1) pg ON dnt.name = pg.name - LEFT JOIN (select * from rnaseqgenes where rn = 1) rg ON dnt.name = rg.dataset_name + INNER JOIN datasetdatasource dd ON o.component_taxon_id = dd.taxon_id + INNER JOIN datasetpresenter dsp ON dd.dataset_presenter_id = dsp.dataset_presenter_id + INNER JOIN sequences sa ON dd.taxon_id = sa.taxon_id + LEFT JOIN (select * from proteomicsgenes where rn = 1) pg ON dd.name = pg.name + LEFT JOIN (select * from rnaseqgenes where rn = 1) rg ON dd.name = rg.dataset_name WHERE sa.rn = 1 ) SELECT DISTINCT @@ -8087,7 +8087,7 @@ delete from &prefixGeneProduct&1 where product is null AND ps.study_name not like '%htseq-intersection-strict%' UNION -- Splice Site data - SELECT ga.source_id, dnt.dataset_presenter_id as dataset_id, + SELECT ga.source_id, dd.dataset_presenter_id as dataset_id, cast (case when ps.profile_set_suffix is null then ps.protocol_app_node_name else ps.protocol_app_node_name || ' ' || ps.profile_set_suffix @@ -8101,19 +8101,19 @@ delete from &prefixGeneProduct&1 where product is null FROM results.NaFeatureExpression nfe, GeneAttributes ga, study.ProtocolAppNode pan, ProfileSamples ps, study.nodeSet s, sres.ExternalDatabaseRelease r, sres.ExternalDatabase d, - DatasetNameTaxon dnt,DatasetProperty dp + DatasetDatasource dd, DatasetProperty dp WHERE ga.na_feature_id = nfe.na_feature_id AND nfe.protocol_app_node_id = pan.protocol_app_node_id AND pan.protocol_app_node_id = ps.protocol_app_node_id AND ps.study_id = s.node_set_id AND s.external_database_release_id = r.external_database_release_id AND r.external_database_id = d.external_database_id - AND d.name = dnt.name - AND dnt.dataset_presenter_id = dp.dataset_presenter_id + AND d.name = dd.name + AND dd.dataset_presenter_id = dp.dataset_presenter_id AND dp.property = 'type' and substr(dp.value, 1, 10) = 'Splice Site' UNION -- microarray expression, quantitative proteomics, and eQTL - SELECT ga.source_id, dnt.dataset_presenter_id as dataset_id, + SELECT ga.source_id, dd.dataset_presenter_id as dataset_id, cast (case when ps.profile_set_suffix is null then ps.protocol_app_node_name else ps.protocol_app_node_name || ' ' || ps.profile_set_suffix @@ -8129,15 +8129,15 @@ delete from &prefixGeneProduct&1 where product is null FROM results.NaFeatureExpression nfe, GeneAttributes ga, study.ProtocolAppNode pan, ProfileSamples ps, study.nodeSet s, sres.ExternalDatabaseRelease r, sres.ExternalDatabase d, - DatasetNameTaxon dnt, DatasetPresenter dsp + DatasetDatasource dd, DatasetPresenter dsp WHERE ga.na_feature_id = nfe.na_feature_id AND nfe.protocol_app_node_id = pan.protocol_app_node_id AND pan.protocol_app_node_id = ps.protocol_app_node_id AND ps.study_id = s.node_set_id AND s.external_database_release_id = r.external_database_release_id AND r.external_database_id = d.external_database_id - AND d.name = dnt.name - AND dnt.dataset_presenter_id = dsp.dataset_presenter_id + AND d.name = dd.name + AND dd.dataset_presenter_id = dsp.dataset_presenter_id AND dsp.subtype != 'rnaseq' ]]>