AbArray And CL EDA

Model/lib/dst/cellularLocalization.dst

@@ -18,8 +18,9 @@ prop=cellularLocalizationWdkAttributes
         <paramRef ref="geneParams.eda_dataset_id" default="${presenterId}" visible="false"/>
         <paramRef ref="geneParams.eda_analysis_spec" allowEmpty="true" prompt="Filter genes based on cellular localization data"/>
 
+<!-- TODO - add in attributesList, when available: ${cellularLocalizationWdkAttributes} -->
          <attributesList
-              summary="organism,gene_location_text,gene_product,${cellularLocalizationWdkAttributes}"
+              summary="organism,gene_location_text,gene_product"
         />
 
 	<summary><![CDATA[

Model/lib/dst/expression.dst

@@ -12,32 +12,22 @@ prop=projectName
              <column name="term"/>
           <sql>
            <![CDATA[
-select s.study_id as internal
+select distinct s.node_set_id as internal
      , s.name as term
-     , s.name as display
-from study.study s
-where name = '${datasetName}'
-
-/**
-select distinct s.study_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
-**/
-
             ]]>
           </sql>
         </sqlQuery>

Model/lib/dst/metaCycle.dst

@@ -68,11 +68,12 @@ prop=includeProjectsExcludeEuPathDB
              <column name="term"/>
           <sql>
            <![CDATA[
-
 	   SELECT s.name as internal, REPLACE (s.name, ' MetaCycle', '') as term
-	   FROM STUDY.STUDY s, STUDY.STUDY i
-	   WHERE i.name = '${datasetName}'
-	   AND i.study_id = s.INVESTIGATION_ID and s.name like '%MetaCycle%'
+     FROM STUDY.nodeset s, sres.externaldatabase ed, sres.externaldatabaserelease edr
+	   WHERE ed.name = '${datasetName}'
+     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','microarray')
             ]]>
           </sql>
         </sqlQuery>

Model/lib/dst/quantProteomics.dst

@@ -83,17 +83,17 @@ prop=dataType
              <column name="internal"/>
              <column name="term"/>
           <sql>
-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
           </sql>
         </sqlQuery>
 

Model/lib/dst/rnaSeqTemplates.dst

@@ -652,7 +652,7 @@ prop=includeProjectsExcludeEuPathDB
            <![CDATA[
 SELECT 'https://${projectName}.org/a/app/record/dataset/' || dataset_presenter_id as internal,
         'https://${projectName}.org/a/app/record/dataset/' || dataset_presenter_id as term
-FROM ApidbTuning.DatasetPresenter
+FROM ApidbTuning.DatasetDatasource
 WHERE name = '${datasetName}'
             ]]>
           </sql>
@@ -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, ' ${antisense}')  THEN  '- Antisense'
        ELSE 'unstranded' END AS sense
-from study.study s
+from study.nodeset s
    , SRES.EXTERNALDATABASERELEASE r
    , sres.externaldatabase d
 where lower(s.name) like '%deseq%'
@@ -807,13 +807,8 @@ prop=includeProjectsExcludeEuPathDB
            <![CDATA[
 	    SELECT num AS internal, num ||' hours' AS term, num ||' hours' AS display
 	    FROM
-	    (SELECT Rownum num
- 	     CONNECT BY Rownum <= '${profileTimeShift}'
-	     UNION
-	     SELECT 0 num
-	     UNION
-	     SELECT Rownum * (-1) num
-	     CONNECT BY Rownum <= '${profileTimeShift}'
+	    (SELECT generate_series(-${profileTimeShift}.0::integer, ${profileTimeShift}.0::integer) 
+             AS num ORDER BY num
 	    ) t
 	    ORDER BY t.num ASC
             ]]>
@@ -1154,11 +1149,12 @@ prop=includeProjectsExcludeEuPathDB
              <column name="term"/>
           <sql>
            <![CDATA[
-
 	   SELECT s.name as internal, REPLACE (s.name, ' MetaCycle', '') as term
-	   FROM STUDY.STUDY s, STUDY.STUDY i
-	   WHERE i.name = '${datasetName}'
-	   AND i.study_id = s.INVESTIGATION_ID and s.name like '%MetaCycle%'
+     FROM STUDY.nodeset s, sres.externaldatabase ed, sres.externaldatabaserelease edr
+	   WHERE ed.name = '${datasetName}'
+     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')
             ]]>
           </sql>
         </sqlQuery>

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 $$;
 

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;
 

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

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

Model/lib/wdk/model/questions/compoundQuestions.xml

@@ -1,7 +1,6 @@
 <wdkModel>
 
-  <questionSet name="CompoundQuestions" displayName="Search for Compounds"
-	       excludeProjects="EuPathDB,UniDB">
+  <questionSet name="CompoundQuestions" displayName="Search for Compounds">
 
     <!--++++++++++++++++++++++++++++++++++++++++++++++++-->
     <!-- Id -->

Model/lib/wdk/model/questions/geneQuestions.xml

@@ -1617,7 +1617,7 @@ IMPORTANT:
          searchCategory="Protein Expression"
          queryRef="GeneId.GenesByMassSpec"
          recordClassRef="TranscriptRecordClasses.TranscriptRecordClass">
-        <attributesList 
+        <attributesList  excludeProjects="EuPathDB"
               summary="gene_location_text,gene_product,sample_count,sum_sequence_count,unique_sequence_count"
               sorting="unique_sequence_count desc"
         /> 
@@ -2507,7 +2507,7 @@ Find genes based on the Gene Ontology (GO) Term(s) or ID(s) assigned to them.
   <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
 
 
-    <question name="GenesByMetabolicPathway"  newBuild="17"  excludeProjects="EuPathDB,UniDB"
+    <question name="GenesByMetabolicPathway"  newBuild="17"
          displayName="Metabolic Pathway"
          shortDisplayName="Metabol Path"
          searchCategory="Putative Function"
@@ -2625,7 +2625,7 @@ Find genes based on the Gene Ontology (GO) Term(s) or ID(s) assigned to them.
   <!-- Genes by Compounds -->
   <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
 
-    <question name="GenesByReactionCompounds" newBuild="17" excludeProjects="EuPathDB,UniDB"
+    <question name="GenesByReactionCompounds" newBuild="17" 
          displayName="Substrates/Products"
          shortDisplayName="Substrs/Prods"
          searchCategory="Putative Function"
@@ -3464,7 +3464,7 @@ The P value is the probability that the binding site with that score would match
         </dynamicAttributes>
     </question>
 
-    <question name="GenesBySingleCell" includeProjects="TriTrypDB,PlasmoDB,PiroplasmaDB,ToxoDB,HostDB,CryptoDB,EuPathDB"
+    <question name="GenesBySingleCell" includeProjects="TriTrypDB,PlasmoDB,PiroplasmaDB,ToxoDB,HostDB,CryptoDB,UniDB"
         displayName="Single Cell RNA-Seq Evidence"
         shortDisplayName="SingleCell"
         searchCategory="Transcriptomics"
@@ -6155,7 +6155,7 @@ Each point shows the sense fold-change and the antisense fold-change between a p
         </propertyList>
 
         <propertyList name="datasetCategory">
-          <value>Protein interactions</value>
+          <value>Y2H interactions</value>
         </propertyList>
 
         <propertyList name="datasetType">
@@ -6315,7 +6315,7 @@ Each point shows the sense fold-change and the antisense fold-change between a p
         </propertyList>
 
         <propertyList name="datasetCategory">
-          <value>LongReadRNASeq</value>
+          <value>longReadrnaseq</value>
         </propertyList>
 
         <propertyList name="datasetType">
@@ -6393,7 +6393,7 @@ Each point shows the sense fold-change and the antisense fold-change between a p
         </propertyList>
 
         <propertyList name="datasetCategory">
-          <value>Protein expression</value>
+          <value>Protein expression (quantitative)</value>
         </propertyList>
 
         <propertyList name="datasetType">

Model/lib/wdk/model/questions/params/compoundParams.xml

@@ -1,5 +1,5 @@
 <wdkModel>
-  <paramSet name="compoundParams" excludeProjects="EuPathDB,UniDB">
+  <paramSet name="compoundParams">
 
     <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
     <!-- Compound IDs -->  
@@ -289,7 +289,7 @@ lower expression in the comparator as compared to the reference.</li>
   <!-- Vocab queries  -->
   <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
 
-  <querySet name="CompoundVQ" queryType="vocab"  isCacheable="true" excludeProjects="EuPathDB,UniDB">
+  <querySet name="CompoundVQ" queryType="vocab"  isCacheable="true">
 
          <sqlQuery name="CompoundID">
             <column name="internal" />
@@ -309,9 +309,9 @@ lower expression in the comparator as compared to the reference.</li>
              <column name="internal"/>
 			 <column name="term"/>
           <sql>
-          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'
           </sql>
 	  </sqlQuery>
@@ -323,12 +323,10 @@ lower expression in the comparator as compared to the reference.</li>
             <column name="term"/>
          <sql>
             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'
 		 </sql>
  </sqlQuery>