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Canned queries - postgres and partitions #245

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33 changes: 18 additions & 15 deletions Model/lib/perl/CannedQuery/ElementNamesWithMetaData.pm
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Expand Up @@ -55,21 +55,24 @@ sub init {

$Self->setSql(<<Sql);

select rownum as element_order, ps.NAME, ps.FACET, ps.CONTXAXIS FROM (
SELECT distinct s.protocol_app_node_name AS name, s.NODE_ORDER_NUM, m1.string_value as facet, m2.string_value as contXAxis
FROM apidbtuning.ProfileSamples s
, apidbtuning.metadata m1
, apidbtuning.metadata m2
WHERE s.study_name = \'<<ProfileSet>>\'
AND s.profile_type = \'<<ProfileType>>\'
--AND m1.study_name(+) = s.study_name
and m1.PAN_ID(+) = s.PROTOCOL_APP_NODE_ID
and m1.property_source_id(+) = \'$facet1\'
--AND m2.study_name(+) = s.study_name
and m2.PAN_ID(+) = s.PROTOCOL_APP_NODE_ID
and m2.property_source_id(+) = \'<<ContXAxis>>\'
ORDER BY s.node_order_num
) ps
SELECT DISTINCT
s.protocol_app_node_name AS name,
s.NODE_ORDER_NUM,
m1.string_value AS facet,
m2.string_value AS contXAxis
FROM apidbtuning.ProfileSamples s
LEFT JOIN apidbtuning.metadata m1
ON m1.PAN_ID = s.PROTOCOL_APP_NODE_ID
AND m1.property_source_id = '$facet1'
--AND m1.study_name = s.study_name
LEFT JOIN apidbtuning.metadata m2
ON m2.PAN_ID = s.PROTOCOL_APP_NODE_ID
AND m2.property_source_id = '<<ContXAxis>>'
--AND m2.study_name = s.study_name
WHERE s.study_name = '<<ProfileSet>>'
AND s.profile_type = '<<ProfileType>>'
ORDER BY s.node_order_num;


Sql

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12 changes: 8 additions & 4 deletions Model/lib/perl/CannedQuery/MultiProfile.pm
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Expand Up @@ -46,19 +46,21 @@ sub init {

$Self->SUPER::init($Args);

$Self->setCollated(1);
$Self->setCollated(1);

$Self->setId ( $Args->{Id } );
$Self->setProfileSet ( $Args->{ProfileSet } );
$Self->setId ( $Args->{Id } );
$Self->setOrgAbbrev($Args->{OrgAbbrev});
$Self->setProfileSet ( $Args->{ProfileSet } );

$Self->setSql(<<Sql);
SELECT p.source_id
, profile_as_string
FROM apidb.Profile p
FROM apidb.Profile_p p
, apidb.ProfileSet ps
WHERE p.source_id in (<<IdList>>)
AND p.profile_set_id = ps.profile_set_id
AND ps.name = '<<ProfileSet>>'
AND p.org_abbrev = '<<OrgAbbrev>>'
Sql

return $Self;
Expand All @@ -72,6 +74,8 @@ sub setId { $_[0]->{'Id' } = $_[1]; $_[0] }
sub getProfileSet { $_[0]->{'ProfileSet' } }
sub setProfileSet { $_[0]->{'ProfileSet' } = $_[1]; $_[0] }

sub getOrgAbbrev { $_[0]->{'OrgAbbrev' } }
sub setOrgAbbrev { $_[0]->{'OrgAbbrev' } = $_[1]; $_[0] }
# ========================================================================
# --------------------------- Support Methods ----------------------------
# ========================================================================
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7 changes: 3 additions & 4 deletions Model/lib/perl/CannedQuery/PathwayGeneraData.pm
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Expand Up @@ -31,11 +31,10 @@ from (select distinct genus
from dots.AaSequenceEnzymeClass asec, sres.EnzymeClass ec
where ec.enzyme_class_id = asec.enzyme_class_id
and ec.ec_number LIKE REPLACE(REPLACE(REPLACE(REPLACE(lower('<<Id>>'),' ',''),'-', '%'),'*','%'),'any','%')
) ec,
(
) ec
RIGHT JOIN (
<<Genera>>
) orgs
where orgs.genus = ec.genus (+)
) orgs ON orgs.genus = ec.genus
order by orgs.o asc
Sql

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5 changes: 4 additions & 1 deletion Model/lib/perl/CannedQuery/PhenotypeRankedNthNames.pm
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Expand Up @@ -14,6 +14,7 @@ sub init {
$Self->SUPER::init($Args);

$Self->setId($Args->{Id});
$Self->setOrgAbbrev($Args->{OrgAbbrev});
$Self->setSourceIdValueQuery($Args->{SourceIdValueQuery});
$Self->setN($Args->{N});

Expand All @@ -31,7 +32,7 @@ select t.value, rownum rn, source_id
from (select source_id, value from dat order by value) t
)
where ('<<Id>>' = 'ALL' AND (rn = 1 or rn = (select ct.m from ct) or mod(rn, round((select ct.m from ct)/<<N>>,0)) = 0))
OR '<<Id>>' = source_id
OR ('<<Id>>' = source_id and '<<OrgAbbrev>>' = org_abbrev)
Sql

return $Self;
Expand All @@ -47,6 +48,8 @@ sub getSourceIdValueQuery{ $_[0]->{_SourceIdValueQuery} }
sub setN { $_[0]->{_n} = $_[1] }
sub getN { $_[0]->{_n} }

sub getOrgAbbrev { $_[0]->{'OrgAbbrev' } }
sub setOrgAbbrev { $_[0]->{'OrgAbbrev' } = $_[1]; $_[0] }

sub prepareDictionary {
my $Self = shift;
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5 changes: 4 additions & 1 deletion Model/lib/perl/CannedQuery/PhenotypeRankedNthSourceIdNames.pm
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Expand Up @@ -14,6 +14,7 @@ sub init {
$Self->SUPER::init($Args);

$Self->setId($Args->{Id});
$Self->setOrgAbbrev($Args->{OrgAbbrev});
$Self->setSourceIdValueQuery($Args->{SourceIdValueQuery});
$Self->setN($Args->{N});

Expand All @@ -31,7 +32,7 @@ select t.value, rownum rn, source_id
from (select source_id, value from dat order by value) t
)
where ('<<Id>>' = 'ALL' AND (rn = 1 or rn = (select ct.m from ct) or mod(rn, round((select ct.m from ct)/<<N>>,0)) = 0))
OR '<<Id>>' = source_id
OR ('<<Id>>' = source_id and '<<OrgAbbrev>>' = org_abbrev)
Sql

return $Self;
Expand All @@ -47,6 +48,8 @@ sub getSourceIdValueQuery{ $_[0]->{_SourceIdValueQuery} }
sub setN { $_[0]->{_n} = $_[1] }
sub getN { $_[0]->{_n} }

sub getOrgAbbrev { $_[0]->{'OrgAbbrev' } }
sub setOrgAbbrev { $_[0]->{'OrgAbbrev' } = $_[1]; $_[0] }

sub prepareDictionary {
my $Self = shift;
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5 changes: 4 additions & 1 deletion Model/lib/perl/CannedQuery/PhenotypeRankedNthValues.pm
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Expand Up @@ -14,6 +14,7 @@ sub init {
$Self->SUPER::init($Args);

$Self->setId($Args->{Id});
$Self->setOrgAbbrev($Args->{OrgAbbrev});
$Self->setSourceIdValueQuery($Args->{SourceIdValueQuery});
$Self->setN($Args->{N});

Expand All @@ -31,7 +32,7 @@ select t.value, rownum rn, source_id
from (select source_id, value from dat order by value) t
)
where ('<<Id>>' = 'ALL' AND (rn = 1 or rn = (select ct.m from ct) or mod(rn, round((select ct.m from ct)/<<N>>,0)) = 0))
OR '<<Id>>' = source_id
OR ('<<Id>>' = source_id AND '<<OrgAbbrev>>' = org_abbrev)
Sql

return $Self;
Expand All @@ -47,6 +48,8 @@ sub getSourceIdValueQuery{ $_[0]->{_SourceIdValueQuery} }
sub setN { $_[0]->{_n} = $_[1] }
sub getN { $_[0]->{_n} }

sub getOrgAbbrev { $_[0]->{'OrgAbbrev' } }
sub setOrgAbbrev { $_[0]->{'OrgAbbrev' } = $_[1]; $_[0] }

sub prepareDictionary {
my $Self = shift;
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6 changes: 5 additions & 1 deletion Model/lib/perl/CannedQuery/Profile.pm
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Expand Up @@ -55,10 +55,11 @@ sub init {

$Self->setSql(<<Sql);
SELECT profile_AS_STRING
FROM apidbtuning.Profile p
FROM apidbtuning.Profile_p p
WHERE p.source_id = '<<Id>>'
AND p.profile_set_name = '<<ProfileSet>>'
AND p.profile_type = '<<ProfileType>>'
AND p.org_abbrev = '<<OrgAbbrev>>'
Sql

return $Self;
Expand All @@ -69,6 +70,9 @@ Sql
sub getId { $_[0]->{'Id' } }
sub setId { $_[0]->{'Id' } = $_[1]; $_[0] }

sub getOrgAbbrev { $_[0]->{'OrgAbbrev' } }
sub setOrgAbbrev { $_[0]->{'OrgAbbrev' } = $_[1]; $_[0] }

sub getSecondaryId { $_[0]->{'SecondaryId' } }
sub setSecondaryId { $_[0]->{'SecondaryId' } = $_[1]; $_[0] }

Expand Down
3 changes: 2 additions & 1 deletion Model/lib/perl/CannedQuery/ProfileByEC.pm
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Expand Up @@ -13,7 +13,7 @@ sub init {

$Self->setSql(<<Sql);
select p.source_id, ec.ec_number, p.profile_as_string
from apidbtuning.profile p,
from apidbtuning.profile_p p,
(SELECT DISTINCT ta.gene_source_id, ec.ec_number
FROM dots.aaSequenceEnzymeClass asec, sres.enzymeClass ec,webready.TranscriptAttributes_p ta
WHERE ta.aa_sequence_id = asec.aa_sequence_id
Expand All @@ -22,6 +22,7 @@ sub init {
) ec
WHERE p.profile_set_name = '<<ProfileSet>>'
AND p.profile_type = '<<ProfileType>>'
AND p.org_abbrev = '<<OrgAbbrev>>'
AND p.source_id = ec.gene_source_id


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10 changes: 7 additions & 3 deletions Model/lib/perl/CannedQuery/ProfileForOligoFromGene.pm
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Expand Up @@ -46,16 +46,18 @@ sub init {

$Self->SUPER::init($Args);

$Self->setId ( $Args->{Id } );
$Self->setProfileSet ( $Args->{ProfileSet } );
$Self->setId ( $Args->{Id } );
$Self->setProfileSet ( $Args->{ProfileSet } );
$Self->setOrgAbbrev($Args->{OrgAbbrev});

$Self->setSql(<<Sql);
SELECT profile_AS_STRING
FROM apidb.Profile p
FROM apidb.Profile_p p
, apidb.ProfileSet ps
WHERE p.source_id = '<<Id>>'
AND p.profile_set_id = ps.profile_set_id
AND ps.name = '<<ProfileSet>>'
AND p.org_abbrev = '<<OrgAbbrev>>'
Sql

return $Self;
Expand All @@ -69,6 +71,8 @@ sub setId { $_[0]->{'Id' } = $_[1]; $_[0] }
sub getProfileSet { $_[0]->{'ProfileSet' } }
sub setProfileSet { $_[0]->{'ProfileSet' } = $_[1]; $_[0] }

sub getOrgAbbrev { $_[0]->{'OrgAbbrev' } }
sub setOrgAbbrev { $_[0]->{'OrgAbbrev' } = $_[1]; $_[0] }
# ========================================================================
# --------------------------- Support Methods ----------------------------
# ========================================================================
Expand Down
9 changes: 6 additions & 3 deletions Model/lib/perl/CannedQuery/ProfileSet.pm
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Expand Up @@ -43,15 +43,17 @@ sub init {

$Self->setCollated(1);

$Self->setProfileSet ( $Args->{ProfileSet } );
$Self->setOrgAbbrev($Args->{OrgAbbrev});
$Self->setProfileSet ( $Args->{ProfileSet } );

$Self->setSql(<<Sql);
SELECT source_id as column_name
, profile_AS_STRING
FROM apidb.Profile p
FROM apidb.Profile_p p
, apidb.ProfileSet ps
WHERE p.profile_set_id = ps.profile_set_id
AND ps.name = '<<ProfileSet>>'
AND p.org_abbrev = '<<OrgAbbrev>>'
Sql

return $Self;
Expand All @@ -61,7 +63,8 @@ Sql

sub getId { $_[0]->{'Id' } }
sub setId { $_[0]->{'Id' } = $_[1]; $_[0] }

sub getOrgAbbrev { $_[0]->{'OrgAbbrev' } }
sub setOrgAbbrev { $_[0]->{'OrgAbbrev' } = $_[1]; $_[0] }
sub getProfileSet { $_[0]->{'ProfileSet' } }
sub setProfileSet { $_[0]->{'ProfileSet' } = $_[1]; $_[0] }

Expand Down
6 changes: 4 additions & 2 deletions Model/lib/perl/CannedQuery/RankedNthRatioValues.pm
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Expand Up @@ -14,6 +14,7 @@ sub init {
$Self->SUPER::init($Args);

$Self->setId($Args->{Id});
$Self->setOrgAbbrev($Args->{OrgAbbrev});
$Self->setSourceIdValueQuery($Args->{SourceIdValueQuery});
$Self->setN($Args->{N});

Expand All @@ -31,7 +32,7 @@ select t.value, rownum rn, source_id, num, denom
from (select source_id, value, num, denom from dat order by value) t
)
where ('<<Id>>' = 'ALL' AND (rn = 1 or rn = (select ct.m from ct) or mod(rn, round((select ct.m from ct)/<<N>>,0)) = 0))
OR '<<Id>>' = source_id
OR ('<<Id>>' = source_id and '<<OrgAbbrev>>' = org_abbrev)
Sql

return $Self;
Expand All @@ -40,7 +41,8 @@ Sql

sub getId { $_[0]->{'Id' } }
sub setId { $_[0]->{'Id' } = $_[1]; $_[0] }

sub getOrgAbbrev { $_[0]->{'OrgAbbrev' } }
sub setOrgAbbrev { $_[0]->{'OrgAbbrev' } = $_[1]; $_[0] }
sub setSourceIdValueQuery { $_[0]->{_SourceIdValueQuery} = $_[1] }
sub getSourceIdValueQuery{ $_[0]->{_SourceIdValueQuery} }

Expand Down
4 changes: 3 additions & 1 deletion Model/lib/perl/CannedQuery/SenseAntisense.pm
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Expand Up @@ -13,6 +13,7 @@ sub init {

$Self->setProfileSetId($Args->{ProfileSetId});
$Self->setId($Args->{Id});
$Self->setOrgAbbrev($Args->{OrgAbbrev});
$Self->setAntisenseFloor($Args->{AntisenseFloor});

return $Self;
Expand All @@ -24,7 +25,8 @@ sub getId { $_[0]->{'Id' } }
sub setId { $_[0]->{'Id' } = $_[1]; $_[0] }
sub getAntisenseFloor { $_[0]->{'AntisenseFloor' } }
sub setAntisenseFloor { $_[0]->{'AntisenseFloor' } = $_[1]; $_[0] }

sub getOrgAbbrev { $_[0]->{'OrgAbbrev' } }
sub setOrgAbbrev { $_[0]->{'OrgAbbrev' } = $_[1]; $_[0] }

sub prepareDictionary {
my $Self = shift;
Expand Down
4 changes: 3 additions & 1 deletion Model/lib/perl/CannedQuery/SenseAntisenseX.pm
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Expand Up @@ -21,6 +21,7 @@ with comp as (select ps.node_order_num,ps.protocol_app_node_name,na.value
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='<<Id>>')
, ref as (select ps.node_order_num,ps.protocol_app_node_name,na.value
from apidbtuning.ProfileSamples ps
Expand All @@ -30,7 +31,8 @@ with comp as (select ps.node_order_num,ps.protocol_app_node_name,na.value
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='<<Id>>')
and ga.org_abbrev ='<<OrgAbbrev>>'
and ga.source_id='<<Id>>')
select CONTXAXIS, NAME, ROW_NUMBER() OVER (order by NAME) as element_order
from ( select
ref.protocol_app_node_name || '->' || comp.protocol_app_node_name as NAME
Expand Down
4 changes: 3 additions & 1 deletion Model/lib/perl/CannedQuery/SenseAntisenseY.pm
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Expand Up @@ -21,6 +21,7 @@ with comp as (select ps.node_order_num,ps.protocol_app_node_name,na.value
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='<<Id>>')
, ref as (select ps.node_order_num,ps.protocol_app_node_name,na.value
from apidbtuning.ProfileSamples ps
Expand All @@ -30,7 +31,8 @@ with comp as (select ps.node_order_num,ps.protocol_app_node_name,na.value
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='<<Id>>')
and ga.org_abbrev ='<<OrgAbbrev>>'
and ga.source_id='<<Id>>')
select value, ROW_NUMBER() OVER (order by name) as element_order
from ( select
ref.protocol_app_node_name || '->' || comp.protocol_app_node_name as name
Expand Down
4 changes: 4 additions & 0 deletions Model/lib/perl/CannedQuery/UDProfileValues.pm
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Expand Up @@ -12,6 +12,7 @@ sub init {
$Self->SUPER::init($Args);

$Self->setId($Args->{Id});
$Self->setOrgAbbrev($Args->{OrgAbbrev});
$Self->setProfileSetId($Args->{ProfileSetId});

$Self->setSql(<<Sql);
Expand All @@ -23,6 +24,7 @@ where pan.profile_set_id = '<<ProfileSetId>>'
and pan.protocol_app_node_id = e.protocol_app_node_id
and ga.na_feature_id = e.na_feature_id
and ga.source_id = '<<Id>>'
and ga.org_abbrev = '<<OrgAbbrev>>'
order by pan.node_order_num, pan.protocol_app_node_id
Sql

Expand All @@ -35,6 +37,8 @@ sub setId { $_[0]->{'Id' } = $_[1]; $_[0] }
sub getProfileSetId { $_[0]->{'ProfileSetId' } }
sub setProfileSetId { $_[0]->{'ProfileSetId' } = $_[1]; $_[0] }

sub getOrgAbbrev { $_[0]->{'OrgAbbrev' } }
sub setOrgAbbrev { $_[0]->{'OrgAbbrev' } = $_[1]; $_[0] }

sub prepareDictionary {
my $Self = shift;
Expand Down