I'm wondering if the exception below is a consequence of the ordering of
execution within jooq (or the gradle plugin?). Or are stderr and stdout
conspiring to confuse me.
Today for the first time in a while I had some new DDL to run. I use
flyway(6.3.2) for that and follow up with nu.studer.jooq(5.2). The
latter completed "successfully" but did show this stacktrace within the
log output (abridged here):
INFO: Generating table : Alias.java [input=alias,
output=alias, pk=alias_pkey]
Jun 08, 2021 4:45:35 PM org.jooq.tools.JooqLogger info
INFO: Parse error : Error when parsing column name :
pv(events_less, events_equal, events_greater, 0)
org.jooq.impl.ParserException: Unknown function: [1:4]
pv([*]events_less, events_equal, events_greater, 0)
at org.jooq.impl.ParserContext.exception(ParserImpl.java:12258)
at org.jooq.impl.ParserImpl.parseUnaryOps(ParserImpl.java:6557)
at org.jooq.impl.ParserImpl.parseExp(ParserImpl.java:6521)
at org.jooq.impl.ParserImpl.parseFactor(ParserImpl.java:6498)
at org.jooq.impl.ParserImpl.parseSum(ParserImpl.java:6444)
at org.jooq.impl.ParserImpl.parseNumericOp(ParserImpl.java:6429)
at org.jooq.impl.ParserImpl.parseCollated(ParserImpl.java:6403)
at org.jooq.impl.ParserImpl.parseConcat(ParserImpl.java:6393)
at org.jooq.impl.ParserImpl.parsePredicate(ParserImpl.java:5323)
at org.jooq.impl.ParserImpl.parseNot(ParserImpl.java:5253)
at org.jooq.impl.ParserImpl.parseAnd(ParserImpl.java:5243)
at org.jooq.impl.ParserImpl.parseOr(ParserImpl.java:5234)
at org.jooq.impl.ParserImpl.parseField(ParserImpl.java:6310)
at org.jooq.impl.ParserImpl.parseField(ParserImpl.java:6235)
at org.jooq.impl.ParserImpl.parseField(ParserImpl.java:764)
at org.jooq.impl.ParserImpl.parseField(ParserImpl.java:758)
at
org.jooq.meta.postgres.PostgresDatabase.tryParseColumnName(PostgresDatabase.java:266)
at
org.jooq.meta.postgres.PostgresDatabase.getIndexes0(PostgresDatabase.java:226)
at
org.jooq.meta.AbstractDatabase$14.run(AbstractDatabase.java:2338)
at
org.jooq.meta.AbstractDatabase.onError(AbstractDatabase.java:3094)
at
org.jooq.meta.AbstractDatabase.getIndexes(AbstractDatabase.java:2335)
at
org.jooq.meta.AbstractDatabase.getIndexes(AbstractDatabase.java:2369)
at
org.jooq.meta.AbstractTableDefinition.getIndexes(AbstractTableDefinition.java:99)
at
org.jooq.codegen.JavaGenerator.generateTable(JavaGenerator.java:5327)
at
org.jooq.codegen.JavaGenerator.generateTable(JavaGenerator.java:5038)
at
org.jooq.codegen.JavaGenerator.generateTables(JavaGenerator.java:5012)
at org.jooq.codegen.JavaGenerator.generate(JavaGenerator.java:582)
at org.jooq.codegen.JavaGenerator.generate(JavaGenerator.java:537)
at org.jooq.codegen.JavaGenerator.generate(JavaGenerator.java:436)
at org.jooq.codegen.GenerationTool.run0(GenerationTool.java:879)
at org.jooq.codegen.GenerationTool.run(GenerationTool.java:233)
at
org.jooq.codegen.GenerationTool.generate(GenerationTool.java:228)
at org.jooq.codegen.GenerationTool.main(GenerationTool.java:200)
Jun 08, 2021 4:45:35 PM org.jooq.tools.JooqLogger info
INFO: Indexes fetched : 22 (22 included, 0 excluded)
Jun 08, 2021 4:45:35 PM org.jooq.tools.JooqLogger info
INFO: Generating table : Cytoband.java [input=cytoband,
output=cytoband, pk=N/A]
Funny thing is Alias has no reference to pv() function:
\d base.alias
Table "base.alias"
Column | Type | Collation | Nullable | Default
-----------+------+-----------+----------+---------
id | uuid | | not null |
person_id | uuid | | not null |
aka | text | | not null |
people_id | uuid | | |
akadef_id | uuid | | |
Indexes:
"alias_pkey" PRIMARY KEY, btree (id)
"aliasperpeep" UNIQUE CONSTRAINT, btree (aka, people_id)
Foreign-key constraints:
"alias_people_id_fkey" FOREIGN KEY (people_id) REFERENCES
base.people(id)
"alias_person_id_fkey" FOREIGN KEY (person_id) REFERENCES
base.person(id)
"defcon" FOREIGN KEY (akadef_id) REFERENCES base.definervalue(id)
I believe the only table which mentions that function is Segment:
\d sgstemplate.segment
Table "sgstemplate.segment"
Column | Type | Collation | Nullable | Default
------------------+---------+-----------+----------+---------
id | uuid | | not null |
chrom | integer | | not null |
markerset_id | uuid | | not null |
probandset_id | uuid | | not null |
startbase | integer | | not null |
endbase | integer | | not null |
firstmarker | integer | | not null |
lastmarker | integer | | not null |
events_less | bigint | | not null | 0
events_equal | bigint | | not null | 0
events_greater | bigint | | not null | 0
threshold_events | integer | | |
Indexes:
"segment_pkey" PRIMARY KEY, btree (id)
"useg" UNIQUE, btree (probandset_id, markerset_id, startbase,
endbase) WITH (fillfactor='95')
"fpvx" btree (pv(events_less, events_equal, events_greater, 0))
"segment_markerset_id_idx" btree (markerset_id)
"segment_probandset_id_idx" btree (probandset_id)
Foreign-key constraints:
"segment_markerset_id_fkey" FOREIGN KEY (markerset_id)
REFERENCES base.markerset(id)
"segment_probandset_id_fkey" FOREIGN KEY (probandset_id)
REFERENCES sgstemplate.probandset(id)
Referenced by:
TABLE "sgstemplate.chaseable" CONSTRAINT
"chaseable_segment_id_fkey" FOREIGN KEY (segment_id) REFERENCES
sgstemplate.segment(id)
TABLE "sgstemplate.duo_chaseable" CONSTRAINT
"duo_chaseable_segment1_id_fkey" FOREIGN KEY (segment1_id)
REFERENCES sgstemplate.segment(id)
TABLE "sgstemplate.duo_chaseable" CONSTRAINT
"duo_chaseable_segment2_id_fkey" FOREIGN KEY (segment2_id)
REFERENCES sgstemplate.segment(id)
TABLE "sgstemplate.optimalset_segment" CONSTRAINT
"threshold_segment_threshold_segment_fkey" FOREIGN KEY (segment_id)
REFERENCES sgstemplate.segment(id)
A subsequent run of 'gradle build' says the generateJooq task is
up-to-date.
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