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Re: [GUSDEV] bug in GUS schema, evidentiated by InsertSequenceFeatures
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From: Fernan A. <fe...@ii...> - 2006-10-17 12:35:18
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+----[ an...@ne... <an...@ne...> (17.Oct.2006 05:57):
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| Quoting John Iodice <io...@pc...>:
|=20
| > Can you tell me more about what was happening when the error occurred?
|=20
| The command I was running is the following:
|=20
| ga GUS::Supported::Plugin::InsertSequenceFeatures
| --mapFile /hardmnt/mpa/gus/GUS/gus_home/config/genbank2gus.xml
| --inputFileOrDir CHR_I/NC_003279.gbk --fileFormat Genbank
| --extDbName "NCBI Genome data" --extDbRlsVer 2006.02.16
| --veryVerbose --sqlVerbose
| --commit
|=20
| The error, occurring at the end of the import run, is this one:
|=20
| sqlExec:
| INSERT INTO DoTSVer.SourceVer select v.*,215,now(),30 from DoTS.Source v
| where v.na_feature_id =3D ?
| bindValues (5)
|=20
| DBD::Pg::st execute failed: ERROR: null value in column "na_feature_id"
| violates not-null constraint at
| /hardmnt/mpa/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 14=
7,
| <GEN39> line 368238.
|=20
| The script does import the data anyway, leaving me to wonder if there is =
no
| transaction support (or if it is broken).
Antonio and John,
we're using PostgreSQL with GUS 3.5.1 over here and we've
not seen this error while using the supported ISF plugin.
and I don't remember doing anything weird to our
installation (patching and/or editing).
| > Mike mentioned the install logs; do you still have those? If so,
| > please send me a copy.
|=20
| I haven't got the schema building logs any more, but I attach you the
| objects.sql that produced my schema - as you can see, it is already wrong=
at
| this level: all of the versioned views have incomplete rules for insert a=
nd
| update.
|
| > There are some other people using GUS and PostgreSQL. Do you know
| > why they haven't encountered the error (or how they worked around it)?
|
+----]
[rest of message snipped]
We're one of those. And AFAIR we haven't done anything
special on our installation. I don't remember coming across
this error, but other than that, how can we tell if our
schema is right or if we lack rules for insert/update? I
mean at the psql level ... is this related only to the
dotsver.sourcever table or are more tables involved (see at
the end of this message the information for the
dotsver.sourcever table I got from psql).
Fernan
PS: output of '\d dotsver.sourcever'
View "dotsver.sourcever"
Column | Type | Modifiers=20
------------------------------+-----------------------------+-----------
na_feature_id | numeric(10,0) |=20
na_sequence_id | numeric(10,0) |=20
subclass_view | character varying(30) |=20
name | character varying(30) |=20
sequence_ontology_id | numeric(10,0) |=20
parent_id | numeric(10,0) |=20
external_database_release_id | numeric(10,0) |=20
source_id | character varying(50) |=20
prediction_algorithm_id | numeric(5,0) |=20
is_predicted | numeric(1,0) |=20
review_status_id | numeric(10,0) |=20
cell_line | character varying(4000) |=20
cell_type | character varying(4000) |=20
chromoplast | character varying(4000) |=20
chromosome | character varying(4000) |=20
clone | character varying(4000) |=20
clone_lib | character varying(4000) |=20
cultivar | character varying(4000) |=20
cyanelle | character varying(4000) |=20
dev_stage | character varying(4000) |=20
focus | character varying(4000) |=20
frequency | character varying(4000) |=20
germline | character varying(4000) |=20
haplotype | character varying(4000) |=20
insertion_seq | text |=20
isolate | character varying(4000) |=20
kinetoplast | character varying(4000) |=20
lab_host | character varying(4000) |=20
macronuclear | character varying(4000) |=20
organelle | character varying(4000) |=20
pop_variant | character varying(4000) |=20
plasmid | character varying(4000) |=20
proviral | character varying(4000) |=20
rearranged | character varying(4000) |=20
sequenced_mol | character varying(4000) |=20
serotype | character varying(4000) |=20
sex | character varying(4000) |=20
specific_host | character varying(4000) |=20
strain | character varying(4000) |=20
sub_clone | character varying(4000) |=20
sub_species | character varying(4000) |=20
sub_strain | character varying(4000) |=20
tissue_lib | character varying(4000) |=20
transposon | character varying(4000) |=20
variety | character varying(4000) |=20
virion | character varying(4000) |=20
chloroplast | character varying(4000) |=20
citation | character varying(4000) |=20
map | character varying(4000) |=20
organism | character varying(4000) |=20
specimen_voucher | character varying(4000) |=20
tissue_type | character varying(4000) |=20
usedin | character varying(4000) |=20
label | character varying(4000) |=20
modification_date | timestamp without time zone |=20
user_read | numeric(1,0) |=20
user_write | numeric(1,0) |=20
group_read | numeric(1,0) |=20
group_write | numeric(1,0) |=20
other_read | numeric(1,0) |=20
other_write | numeric(1,0) |=20
row_user_id | numeric(12,0) |=20
row_group_id | numeric(4,0) |=20
row_project_id | numeric(4,0) |=20
row_alg_invocation_id | numeric(12,0) |=20
version_alg_invocation_id | numeric(12,0) |=20
version_date | timestamp without time zone |=20
version_transaction_id | numeric(12,0) |=20
View definition:
SELECT nafeatureimpver.na_feature_id, nafeatureimpver.na_sequence_id, nafe=
atureimpver.subclass_view, nafeatureimpver.name, nafeatureimpver.sequence_o=
ntology_id, nafeatureimpver.parent_id, nafeatureimpver.external_database_re=
lease_id, nafeatureimpver.source_id, nafeatureimpver.prediction_algorithm_i=
d, nafeatureimpver.is_predicted, nafeatureimpver.review_status_id, nafeatur=
eimpver.string1 AS cell_line, nafeatureimpver.string2 AS cell_type, nafeatu=
reimpver.string3 AS chromoplast, nafeatureimpver.string4 AS chromosome, naf=
eatureimpver.string5 AS clone, nafeatureimpver.string6 AS clone_lib, nafeat=
ureimpver.string7 AS cultivar, nafeatureimpver.string8 AS cyanelle, nafeatu=
reimpver.string9 AS dev_stage, nafeatureimpver.string10 AS focus, nafeature=
impver.string11 AS frequency, nafeatureimpver.string12 AS germline, nafeatu=
reimpver.string13 AS haplotype, nafeatureimpver.clob1 AS insertion_seq, naf=
eatureimpver.string14 AS isolate, nafeatureimpver.string15 AS kinetoplast, =
nafeatureimpver.string16 AS lab_host, nafeatureimpver.string17 AS macronucl=
ear, nafeatureimpver.string18 AS organelle, nafeatureimpver.string19 AS pop=
_variant, nafeatureimpver.string20 AS plasmid, nafeatureimpver.string21 AS =
proviral, nafeatureimpver.string22 AS rearranged, nafeatureimpver.string23 =
AS sequenced_mol, nafeatureimpver.string24 AS serotype, nafeatureimpver.str=
ing25 AS sex, nafeatureimpver.string26 AS specific_host, nafeatureimpver.st=
ring27 AS strain, nafeatureimpver.string28 AS sub_clone, nafeatureimpver.st=
ring29 AS sub_species, nafeatureimpver.string30 AS sub_strain, nafeatureimp=
ver.string31 AS tissue_lib, nafeatureimpver.string32 AS transposon, nafeatu=
reimpver.string33 AS variety, nafeatureimpver.string34 AS virion, nafeature=
impver.string35 AS chloroplast, nafeatureimpver.string36 AS citation, nafea=
tureimpver.string37 AS map, nafeatureimpver.string38 AS organism, nafeature=
impver.string39 AS specimen_voucher, nafeatureimpver.string40 AS tissue_typ=
e, nafeatureimpver.string41 AS usedin, nafeatureimpver.string42 AS label, n=
afeatureimpver.modification_date, nafeatureimpver.user_read, nafeatureimpve=
r.user_write, nafeatureimpver.group_read, nafeatureimpver.group_write, nafe=
atureimpver.other_read, nafeatureimpver.other_write, nafeatureimpver.row_us=
er_id, nafeatureimpver.row_group_id, nafeatureimpver.row_project_id, nafeat=
ureimpver.row_alg_invocation_id, nafeatureimpver.version_alg_invocation_id,=
nafeatureimpver.version_date, nafeatureimpver.version_transaction_id
FROM dotsver.nafeatureimpver
WHERE nafeatureimpver.subclass_view::text =3D 'Source'::text;
Rules:
sourcever_72791 AS
ON INSERT TO dotsver.sourcever DO INSTEAD INSERT INTO dotsver.nafeatur=
eimpver (na_feature_id, na_sequence_id, subclass_view, name, sequence_ontol=
ogy_id, parent_id, external_database_release_id, source_id, prediction_algo=
rithm_id, is_predicted, review_status_id, string1, string2, string3, string=
4, string5, string6, string7, string8, string9, string10, string11, string1=
2, string13, clob1, string14, string15, string16, string17, string18, strin=
g19, string20, string21, string22, string23, string24, string25, string26, =
string27, string28, string29, string30, string31, string32, string33, strin=
g34, string35, string36, string37, string38, string39, string40, string41, =
string42, modification_date, user_read, user_write, group_read, group_write=
, other_read, other_write, row_user_id, row_group_id, row_project_id, row_a=
lg_invocation_id, version_alg_invocation_id, version_date, version_transact=
ion_id)=20
VALUES (new.na_feature_id, new.na_sequence_id, new.subclass_view, new.nam=
e, new.sequence_ontology_id, new.parent_id, new.external_database_release_i=
d, new.source_id, new.prediction_algorithm_id, new.is_predicted, new.review=
_status_id, new.cell_line, new.cell_type, new.chromoplast, new.chromosome, =
new.clone, new.clone_lib, new.cultivar, new.cyanelle, new.dev_stage, new.fo=
cus, new.frequency, new.germline, new.haplotype, new.insertion_seq, new.iso=
late, new.kinetoplast, new.lab_host, new.macronuclear, new.organelle, new.p=
op_variant, new.plasmid, new.proviral, new.rearranged, new.sequenced_mol, n=
ew.serotype, new.sex, new.specific_host, new.strain, new.sub_clone, new.sub=
_species, new.sub_strain, new.tissue_lib, new.transposon, new.variety, new.=
virion, new.chloroplast, new.citation, new.map, new.organism, new.specimen_=
voucher, new.tissue_type, new.usedin, new.label, new.modification_date, new=
=2Euser_read, new.user_write, new.group_read, new.group_write, new.other_re=
ad, new.other_write, new.row_user_id, new.row_group_id, new.row_project_id,=
new.row_alg_invocation_id, new.version_alg_invocation_id, new.version_date=
, new.version_transaction_id)
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