Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

ZFIN-9444 fix WashZU accession and have them show the defline plus se… #1268

Merged
merged 2 commits into from
Dec 18, 2024
Merged

ZFIN-9444 fix WashZU accession and have them show the defline plus se… #1268

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
39587cc
ZFIN-9444 fix WashZU accession and have them show the defline plus se…
cmpich Dec 18, 2024
c79b44c
ZFIN-9444 add LB script to master file
cmpich Dec 18, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
20 changes: 1 addition & 19 deletions lib/DB_functions/get_dblink_acc_num_display.sql
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -32,25 +32,7 @@ CREATE OR REPLACE FUNCTION "public"."get_dblink_acc_num_display"("dblinkfdbconti
and fdb_db_pk_id = fdbcont_fdb_db_id;


if (dblinkDbName = 'WashUZ') then
-- we need to prepend 'wz' to the acc_num
dblinkAccNumDisplay := 'wz' || dblinkAccNum;

--replace the miranda acc num with one that looks more like the
--way curators want to display miRNA names at ZFIN.
--ZDB-FDBCONT-090529-1, dre-let-7g
--execute function
--get_dblink_acc_num_display('ZDB-FDBCONT-090529-1','dre-let-7g')

else

-- we need to prepend 'wz' to the acc_num

-- spew out exactly what came in
dblinkAccNumDisplay = dblinkAccNum;

end if;

dblinkAccNumDisplay = dblinkAccNum;
return dblinkAccNumDisplay;
end

Expand Down
46 changes: 46 additions & 0 deletions source/org/zfin/db/postGmakePostloaddb/1165/ZFIN-9444.sql
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,46 @@
--liquibase formatted sql
--changeset cmpich:ZFIN-9444.sql

insert into foreign_db_contains_display_group_member
(fdbcdgm_fdbcont_zdb_id, fdbcdgm_group_id, fdbcdgm_can_view, fdbcdgm_can_add, fdbcdgm_can_edit, fdbcdgm_can_delete)
values ('ZDB-FDBCONT-040412-31', 12, true, true, true, true);

create temp table id
(
id text
);

insert into id
select get_id('BLASTDB');

insert into blast_database
(blastdb_zdb_id, blastdb_name, blastdb_abbrev, blastdb_description, blastdb_public,
blastdb_type, blastdb_tool_display_name,
blastdb_is_being_processed, blastdb_origination_id)
select id,
'Published RNA Washington',
'wz_est',
'EST sequences curated by ZFIN staff from publications.',
false,
'nucleotide',
'Published RNA',
false,
2
from id;

update foreign_db_contains
set fdbcont_primary_blastdb_zdb_id = (select id from id)
where fdbcont_zdb_id = 'ZDB-FDBCONT-040412-31';

update foreign_db
set fdb_db_query = '/action/blast/display-sequence?accession='
where fdb_db_name = 'WashUZ';

update db_link
set dblink_acc_num = db_link.dblink_acc_num_display
where dblink_fdbcont_zdb_id = 'ZDB-FDBCONT-040412-31';

update db_link
set dblink_acc_num = db_link.dblink_acc_num_display,
dblink_info = dblink_info || ', added prefix wz to accession '||CURRENT_DATE
where dblink_fdbcont_zdb_id = 'ZDB-FDBCONT-040412-31';
2 changes: 1 addition & 1 deletion source/org/zfin/db/postGmakePostloaddb/1165/db.changelog.master.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,6 @@
xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog
http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.1.xsd">

<!-- <include file="source/org/zfin/db/postGmakePostloaddb/1165/ZFIN-.....sql" />-->
<include file="source/org/zfin/db/postGmakePostloaddb/1165/ZFIN-9444.sql" />

</databaseChangeLog>
1 change: 1 addition & 0 deletions source/org/zfin/sequence/blast/Database.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -177,6 +177,7 @@ public static enum AvailableAbbrev {
ZFIN_MICRORNA("zfin_microRNA"),
ZFIN_MIRNA_STEMLOOP("zfin_miRNA_stemloop"),
ZFIN_MIRNA_MATURE("zfin_miRNA_mature"),
WZ_EST("wz_est"),
ZFIN_MRPH("zfin_mrph"),
ZFIN_TALEN("zfin_talen"),
ZFIN_CRISPR("zfin_crispr"),
Expand Down
Loading