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Dataplotter partition #145

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8a678e6
adjust dataplotter query
steve-fischer-200 Jan 21, 2026
d28eba0
use org_abbrev in dataplotter
steve-fischer-200 Jan 23, 2026
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22 changes: 16 additions & 6 deletions Model/lib/xml/dataPlotter/queries.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
', ' || dsp.short_attribution, '''', '`') as display_name,
dsp.dataset_presenter_id as presenter_id,
ds.order_num
from apidbTuning.Profile p,
from apidbTuning.Profile_p p,
apidbTuning.ProfileSamples ps,
study.ProtocolAppNode pan,
apidbtuning.datasetdatasource dd,
Expand All @@ -23,6 +23,7 @@
and p.dataset_subtype = 'rnaseq'
and p.profile_type = 'values'
and p.source_id = '$id'
and p.org_abbrev = '$orgAbbrev'
and ((dprop.value = 'false'
and pan.name like '%firststrand%')
or (dprop.value = 'true'
Expand Down Expand Up @@ -51,26 +52,28 @@
<query name="profile_set_names">
<![CDATA[
select DISTINCT pt.profile_set_name || ' [' || pt.node_type || ']' as profile_set_name,
profile_type
profile_type, abbrev as org_abbrev
from apidbtuning.profiletype pt
, (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::NAFeatureExpression') dr
, apidbtuning.Datasetdatasource dd
, apidb.organism o
where dd.dataset_presenter_id = '$datasetPresenterId'
and pt.dataset_name = dd.name
and pt.profile_study_id = dr.node_set_id
and pt.profile_set_name NOT like '%PaGE%'
and dd.taxon_id = o.taxon_id
]]>
</query>

<query name="profile_set_names_by_source_id">
<![CDATA[
select DISTINCT pt.profile_set_name || ' [' || pt.node_type || ']' as profile_set_name
, pt.profile_type
from apidbtuning.profile p
from apidbtuning.profile_p p
, apidbtuning.Datasetdatasource dd
, apidbtuning.profiletype pt
LEFT JOIN (select distinct sl.node_set_id
Expand All @@ -83,6 +86,7 @@
and p.profile_study_id = pt.profile_study_id
and p.profile_type = pt.profile_type
and p.source_id = '$sourceId'
and p.org_abbrev = '$orgAbbrev'
]]>
</query>

Expand All @@ -95,7 +99,7 @@
(select max(rownum) as m
from($sourceIdValueQuery)) ct
where ('$sourceId' = 'ALL' AND (rn = 1 or rn = ct.m or mod(rn, round(ct.m/$N,0)) = 0))
OR '$sourceId' = source_id
OR ('$sourceId' = source_id and '$orgAbbrev' = org_abbrev)
]]>
</query>

Expand Down Expand Up @@ -131,8 +135,9 @@ from (select row_number() OVER () as rn, points.* from (
( select row_number() OVER () as rn, vs.* from (
SELECT profile_study_id, dataset_name, p.profile_set_name, p.profile_type, p.node_type,
unnest( STRING_TO_ARRAY(p.profile_AS_STRING, chr(9) ,'')) as oneval
FROM apidbtuning.Profile p
FROM apidbtuning.Profile_p p
where p.profile_type = 'values'
AND p.org_abbrev = '$orgAbbrev'
AND p.profile_set_name || ' [' || node_type || ']' = '$profileSetName'
) vs
) vals
Expand Down Expand Up @@ -171,6 +176,7 @@ and pts.profile_study_id = vals.profile_study_id
AND ec.ec_number LIKE REPLACE(REPLACE(REPLACE(REPLACE(lower('$sourceId'),' ',''),'-', '%'),'*','%'),'any','%')) ec
WHERE p.profile_set_name || ' [' || node_type || ']' = '$profileSetName'
AND p.profile_type = '$profileType'
AND p.org_abbrev = '$orgAbbrev'
AND p.source_id = ec.gene_source_id) t
, table(cast(multiset(select level from dual connect by level <= length (regexp_replace(t.profile_as_string, '[^' || CHR(9) || ']+')) + 1) as sys.OdciNumberList)) levels) samplevalues
where samplenames.element_order = samplevalues.element_order
Expand Down Expand Up @@ -246,6 +252,7 @@ and pts.profile_study_id = vals.profile_study_id
and ps.profile_type = 'values'
and ps.protocol_app_node_id = na.protocol_app_node_id
and na.na_feature_id = ga.na_feature_id
and ga.org_abbrev='$orgAbbrev',
and ga.source_id='$sourceId') sense_comp
, (select ps.node_order_num, ps.protocol_app_node_name
, na.value
Expand All @@ -256,6 +263,7 @@ and pts.profile_study_id = vals.profile_study_id
and ps.profile_type = 'values'
and ps.protocol_app_node_id = na.protocol_app_node_id
and na.na_feature_id = ga.na_feature_id
and ga.org_abbrev='$orgAbbrev',
and ga.source_id='$sourceId') sense_ref
where sense_comp.protocol_app_node_name != sense_ref.protocol_app_node_name) sense
, (select antisense_ref.protocol_app_node_name || '->' || antisense_comp.protocol_app_node_name as name
Expand All @@ -268,6 +276,7 @@ and pts.profile_study_id = vals.profile_study_id
and ps.profile_type = 'values'
and ps.protocol_app_node_id = na.protocol_app_node_id
and na.na_feature_id = ga.na_feature_id
and ga.org_abbrev='$orgAbbrev',
and ga.source_id='$sourceId') antisense_comp
, (select ps.node_order_num,ps.protocol_app_node_name,na.value
from apidbtuning.ProfileSamples ps
Expand All @@ -277,7 +286,8 @@ and pts.profile_study_id = vals.profile_study_id
and ps.profile_type = 'values'
and ps.protocol_app_node_id = na.protocol_app_node_id
and na.na_feature_id = ga.na_feature_id
and ga.source_id='$sourceId') antisense_ref
and ga.org_abbrev='$orgAbbrev',
and ga.source_id='$sourceId') antisense_ref
where antisense_comp.protocol_app_node_name != antisense_ref.protocol_app_node_name) antisense
where sense.name = antisense.name
]]>
Expand Down
11 changes: 11 additions & 0 deletions blig
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Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
ec_number_gene, pathway_id

gene_source_id

gene_source_id, ec_number_gene, pathway_id

pathway_id

complete_ec, exact_match, ext_db_rls, pathway_source_id, pathway_source, gene_source_id, ec_number_gene, ec_number_pathway

gene_source_id, complete_ec, exact_patch, pathway_source