gene products: drop Preferred/Alternate queries; use AllGeneProducts for table

Author: iodice

Model/lib/wdk/ApiCommon/geneQueries.xml

@@ -417,138 +417,12 @@
       <column name="product"/>
       <sql>
       <![CDATA[
-          select 'dots.GeneFeature' as source, source_id, product
-          from dots.GeneFeature
-          where product is not null
-        union
-          select 'dots.TranscriptFeature' as source, gf.source_id, t.product
-          from dots.GeneFeature gf, dots.Transcript t
-          where gf.na_feature_id = t.parent_id
-            and t.product is not null
-        union
-          select 'apidb.GeneFeatureProduct' as source, gf.source_id, gfp.product
-          from dots.GeneFeature gf, apidb.GeneFeatureProduct gfp
-          where gfp.na_feature_id = gf.na_feature_id
-        union
-          select 'apidb.TranscriptProduct' as source, gf.source_id, tp.product
-          from dots.GeneFeature gf, dots.Transcript t,
-               apidb.TranscriptProduct tp
-          where t.parent_id = gf.na_feature_id
-            and tp.na_feature_id = t.na_feature_id
+          select source_id, product
+          from apidbTuning.AllGeneProducts
       ]]>
       </sql>
     </sqlQuery>
 
-
-<!--
-    <sqlQuery name="PreferredProducts" isCacheable="false" >
-      <column name="source_id"/>
-      <column name="transcript_ids"/>
-      <column name="project_id"/>
-      <column name="product"/>
-      <column name="reference" includeProjects="FungiDB,TriTrypDB"/>
-      <column name="evidence_code" includeProjects="FungiDB,TriTrypDB"/>
-      <column name="evidence_code_parameter" includeProjects="FungiDB,TriTrypDB"/>
-      <sql>
-      <![CDATA[
-        /* PreferredProducts: check apidb.TranscriptProduct and
-           apidb.GeneFeatureProduct for records with IS_PREFERRED set. If
-           (and only if) that turns up nothing, check the PRODUCT column of
-           dots.GeneFeature and dots.Transcript */
-        with evids
-             as (select distinct gaiec.go_evidence_code_id, ot.name
-                 from  dots.GoAssocInstEvidCode gaiec, sres.OntologyTerm ot
-                 where ot.ontology_term_id = gaiec.go_evidence_code_id)
-          select ta.gene_source_id as source_id, tp.product, ta.project_id,
-                 listagg(source_id, ', ' on overflow truncate) within group(order by source_id)
-                   as transcript_ids,
-                 listagg(publication, ', ' on overflow truncate) within group(order by source_id)
-                   as reference,
-                 e.name as evidence_code,
-                 tp.with_from AS evidence_code_parameter
-          from apidb.TranscriptProduct tp,
-               apidbTuning.TranscriptAttributes ta, evids e
-          where ta.na_feature_id = tp.na_feature_id
-            and tp.is_preferred = 1
-            and tp.evidence_code = e.go_evidence_code_id(+)
-          group by gene_source_id, ta.project_id, tp.product,
-                   e.name, tp.with_from
-        union
-          select ga.source_id, gfp.product, ga.project_id,
-                 cast (null as varchar2(1)) as transcript_ids,
-                 cast (null as varchar2(1)) as reference,
-                 cast (null as varchar2(1)) as evidence_code,
-                 cast (null as varchar2(1)) as evidence_code_parameter
-          from apidb.GeneFeatureProduct gfp,
-               apidbTuning.GeneAttributes ga
-          where ga.na_feature_id = gfp.na_feature_id
-            and gfp.is_preferred = 1
-          group by source_id, ga.project_id, gfp.product
-        union
-          select *
-          from (select ta.gene_source_id as source_id, ta.transcript_product, ta.project_id,
-                       listagg(source_id, ', ' on overflow truncate) within group(order by source_id)
-                         as transcript_ids,
-                       cast (null as varchar2(1)) as reference,
-                       cast (null as varchar2(1)) as evidence_code,
-                       cast (null as varchar2(1)) as evidence_code_parameter
-                from apidbTuning.TranscriptAttributes ta
-                where ta.transcript_product is not null
-                group by ta.gene_source_id, ta.transcript_product, ta.project_id
-               )
-          where source_id
-                in (  select *
-                      from (  select source_id
-                              from dots.GeneFeature
-                              where product is not null
-                            union
-                              select ga.source_id
-                              from dots.Transcript t, apidbTuning.GeneAttributes ga
-                              where t.product is not null
-                                and t.parent_id = ga.na_feature_id
-                           )
-                    minus
-                      select *
-                      from (  select ta.gene_source_id
-                              from apidb.TranscriptProduct tp, apidbTuning.TranscriptAttributes ta
-                              where tp.na_feature_id = ta.na_feature_id
-                            union
-                              select ga.source_id
-                              from apidb.GeneFeatureProduct gfp, apidbTuning.GeneAttributes ga
-                              where gfp.na_feature_id = ga.na_feature_id
-                           )
-                   )
-      ]]>
-      </sql>
-    </sqlQuery>
-
-    <sqlQuery name="AlternateProducts" >
-      <column name="source_id"/>
-      <column name="product"/>
-      <column name="reference"/>
-      <sql>
-        <![CDATA[
-                select ta.gene_source_id as source_id,
-                       tp.product,
-                       listagg(tp.publication, ', ')
-                         within group(order by tp.publication) as reference
-                from apidbTuning.TranscriptAttributes ta, apidb.TranscriptProduct tp
-                where ta.na_feature_id = tp.na_feature_id
-                and tp.is_preferred = 0
-                group by ta.gene_source_id, ta.source_id, tp.product
-              union
-                select gf.source_id,
-                       gfp.product,
-                       cast (null as varchar2(12)) as reference
-                from dots.GeneFeature gf, apidb.GeneFeatureProduct gfp
-                where gf.na_feature_id = gfp.na_feature_id
-                and gfp.is_preferred = 0
-                group by gf.source_id, gfp.product
-        ]]>
-      </sql>
-    </sqlQuery>
--->
-
     <sqlQuery name="gene_dbrefs">
       <column name="source_id"/>
       <column name="dataset"/>