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Fix TAXONLABEL.linked column type mismatch (smallint → boolean) #404

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Merged
rvosa merged 3 commits into from
Jan 13, 2026
Merged

Fix TAXONLABEL.linked column type mismatch (smallint → boolean) #404

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f4b18a1
Initial plan
Copilot Jan 13, 2026
1f2075e
Fix TAXONLABEL.linked column type from smallint to boolean
Copilot Jan 13, 2026
203c12b
Fix all ORM/database smallint→boolean type mismatches
Copilot Jan 13, 2026
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26 changes: 13 additions & 13 deletions treebase-core/src/main/resources/TBASE2_POSTGRES_CREATION.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ CREATE TABLE analysis
"version" integer,
"name" character varying(255),
notes character varying(2000),
validated smallint,
validated boolean,
study_id bigint,
analysis_order integer
)
Expand Down Expand Up @@ -56,7 +56,7 @@ CREATE TABLE analyzeddata
"type" character(1) NOT NULL,
analyzeddata_id bigint NOT NULL,
"version" integer,
"input" smallint,
"input" boolean,
notes character varying(2000),
treelength integer,
analysisstep_id bigint NOT NULL,
Expand Down Expand Up @@ -399,7 +399,7 @@ CREATE TABLE geneticcode
codeorder character varying(255),
extensions character varying(255),
nucorder character varying(255),
predefined smallint,
predefined boolean,
title character varying(255)
)
WITH (OIDS=FALSE);
Expand Down Expand Up @@ -520,10 +520,10 @@ CREATE TABLE matrix
title character varying(255),
"nchar" integer,
ntax integer,
aligned smallint,
diagonal smallint,
aligned boolean,
diagonal boolean,
triangle character varying(255),
casesensitive smallint,
casesensitive boolean,
matrixdatatype_id bigint,
matrixkind_id bigint,
study_id bigint NOT NULL,
Expand Down Expand Up @@ -581,10 +581,10 @@ CREATE TABLE matrixelement
"type" character(1) NOT NULL,
matrixelement_id bigint NOT NULL,
"version" integer,
andlogic smallint,
andlogic boolean,
compoundvalue character varying(1000),
"value" double precision,
gap smallint,
gap boolean,
matrixcolumn_id bigint,
matrixrow_id bigint,
itemdefinition_id bigint,
Expand Down Expand Up @@ -672,13 +672,13 @@ CREATE TABLE phylotree
phylotree_id bigint NOT NULL,
"version" integer,
tb1_treeid character varying(30),
bigtree smallint,
bigtree boolean,
label character varying(255),
ntax integer,
newickstring text,
nexusfilename character varying(255),
published boolean,
rootedtree smallint,
rootedtree boolean,
title character varying(255),
rootnode_id bigint,
study_id bigint NOT NULL,
Expand Down Expand Up @@ -803,7 +803,7 @@ CREATE TABLE statechangeset
(
statechangeset_id bigint NOT NULL,
"version" integer,
reversible smallint,
reversible boolean,
title character varying(255)
)
WITH (OIDS=FALSE);
Expand Down Expand Up @@ -983,7 +983,7 @@ CREATE TABLE taxonlabel
(
taxonlabel_id bigint NOT NULL,
"version" integer,
linked smallint,
linked boolean,
taxonlabel character varying(255),
study_id bigint,
taxonvariant_id bigint
Expand Down Expand Up @@ -1042,7 +1042,7 @@ CREATE TABLE taxonlabelset
(
taxonlabelset_id bigint NOT NULL,
"version" integer,
taxa smallint,
taxa boolean,
title character varying(255),
study_id bigint
)
Expand Down