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Keith Jolley
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[f9ecaa]
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Version 1.48.4.
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Keith Jolley
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[3ca026]
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Code
Collapse multiple coincident cgSTs in isolate results table
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Keith Jolley
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[9852be]
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Code
Use scheme cache for main results table if large scheme.
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Keith Jolley
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[ff0cf8]
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Code
Support array fields as identifier fields in seqbin uploads.
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Keith Jolley
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[952d24]
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Code
Add message about registering account on failed login.
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Keith Jolley
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[7fee8e]
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Code
Fix hyperlink.
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Keith Jolley
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[245e0a]
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Code
Version 1.48.3.
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Keith Jolley
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[a9b744]
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Code
Add space after comma in list of field values to allow wrapping.
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Keith Jolley
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[05d076]
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Code
Prevent unitialized variable warning.
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Keith Jolley
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[93875b]
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Code
Scheme.pm doesn't know about its instance.
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Keith Jolley
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[9d826f]
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Code
Initiate $self->{'system'}->{'script_name'}.
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Keith Jolley
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[50302b]
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Code
Don't return 'best' match if there zero matches.
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Keith Jolley
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[14d333]
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Code
Cache closest matching profile by scheme.
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Keith Jolley
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[dd6663]
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Code
Return empty string if LIN codes not defined.
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Keith Jolley
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[1ff77e]
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Code
Merge branch '202410_lincode' into develop
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Keith Jolley
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[4e4c80]
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Code
Slightly more efficient to short-cut out at top of loop.
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Keith Jolley
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[1354dd]
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Code
Faster calculation of shortest allele.
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Keith Jolley
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[d85947]
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Code
Get all allele flags and cache if calling multiple times.
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Keith Jolley
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[bd7e39]
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Code
Cache client fields.
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Keith Jolley
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[573398]
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Code
Cache locus attribute field lookup.
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Keith Jolley
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[f4fb8d]
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Code
Include LIN code nicknames on for matching prefixes in seq query.
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Keith Jolley
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[2cfe5a]
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Code
Include LIN code nicknames on isolate info page.
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Keith Jolley
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[048e74]
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Code
Use Pg COPY to create BLAST db FASTA.
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Keith Jolley
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[5a0e13]
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Code
Refactor SequenceQuery::_get_lincode_classification()
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Keith Jolley
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[9e0769]
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Code
Get partial LIN code in sequence query.
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Keith Jolley
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[aee776]
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Code
Merge branch 'develop' into 202409_sequence_query
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Keith Jolley
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[515c52]
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Code
No need to find closest match if we have already found an exact match
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Keith Jolley
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[766491]
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Code
Set max e-value to 0.001.
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Keith Jolley
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[f03953]
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Code
Merge branch 'develop' into 202409_sequence_query
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Keith Jolley
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[b1b5f7]
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Code
Remove obsolete logging.
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Keith Jolley
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[77de3d]
on
Code
Don't use locus common name in sequence query.
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Keith Jolley
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[b159f5]
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Code
Use Pg COPY to extract profiles from database.
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Keith Jolley
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[c889bc]
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Code
Show embargo message for normal users.
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Keith Jolley
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[e236a9]
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Code
Fix date restriction on profile query and viewing profile info page.
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Keith Jolley
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[ffecac]
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Code
Remove Genbank accession option on sequence query and seqbin upload.
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Keith Jolley
committed
[e2b52a]
on
Code
Typo.
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Keith Jolley
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[e9d506]
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Code
Use JQuery.multiselect for merge/update user dropdown boxes.
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Keith Jolley
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[c5d0ca]
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Code
Add restricted view message on isolate query page
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Keith Jolley
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[879fdb]
on
Code
Allow override of optlist values using field.overrides file.
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Keith Jolley
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[9dc189]
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Code
Make sure hidden fields are included when creating new version.
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Keith Jolley
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[57b7ae]
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Code
login_to_show_after_date set in config.xml takes pref over global.
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Keith Jolley
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[619f4d]
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Code
Remove newline.
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Keith Jolley
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[75b2ac]
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Code
Use Pg COPY to create cache.
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Keith Jolley
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[ef6052]
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Code
Mark profile cache stale on automated profile definitions.
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Keith Jolley
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[a21fda]
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Code
Mark profile cache if profile added, deleted, or updated.
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Keith Jolley
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[ee5459]
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Code
Cache profiles to file.
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Keith Jolley
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[242467]
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Code
Version 1.48.2.
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Keith Jolley
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[0999ad]
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Code
REST: Check scheme has PK before running profiles_csv method.
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Keith Jolley
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[74f99f]
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Code
Query to filter profiles on number of mismatches is too slow.
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Keith Jolley
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[58cdf2]
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Code
Merge branch '202409_sequence_query' into 202409_plpgsql
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Keith Jolley
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[00d3ce]
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Code
Use || as FASTA header separator to allow | in allele identifiers.
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Keith Jolley
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[8500c6]
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Code
Increased BLASTN word size to 20 (from 15).
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Keith Jolley
committed
[1a13fb]
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Code
Use allele length from FASTA header in exact match parse.
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Keith Jolley
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[5a3c79]
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Code
Save allele length in FASTA header used to create BLAST db
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Keith Jolley
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[8ed6a6]
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Code
Only check top 20 hits per match length. Check DNA/RNA together.
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Keith Jolley
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[6e644f]
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Code
Cache seq type determination. Use tr/ rather than s/ to remove spaces
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Keith Jolley
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[caeb7f]
on
Code
Cache allele lookups.
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Keith Jolley
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[490860]
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Code
Test plpgsql method alongside existing Perl code.
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Keith Jolley
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[b5773f]
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plpgsql function to lookup profiles.
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Keith Jolley
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[1c4e8d]
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Version 1.48.1.
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Keith Jolley
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[19c8be]
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Use offset and limit when building profile list.
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Keith Jolley
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[e034dc]
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Code
Explicitly use table name when selecting lincodes.profile_id.
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Keith Jolley
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[5c9c40]
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Code
Fix LIN code prefix lookup on profile info and REST profile pages.
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Keith Jolley
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[f77407]
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Code
Version 1.48.0.
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Keith Jolley
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[66e464]
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Code
Remove logging.
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Keith Jolley
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[833103]
on
Code
Fix empty method body when no placeholders defined.
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Keith Jolley
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[222dd9]
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Code
Merge branch '202409_placeholders' into develop
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Keith Jolley
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[559a59]
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Code
Optional placeholder text for scheme/LINcode fields.
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Keith Jolley
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[50a029]
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Code
Add optional placeholder text for provenance and eav fields.
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Keith Jolley
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[be0150]
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Code
Add comment to bigsdb.conf about virtual environment.
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Keith Jolley
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[70e297]
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Code
Need full path to grapetree.
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Keith Jolley
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[0e6ed7]
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Code
Make GrapeTree path consistent with other Python tools.
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Keith Jolley
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[7175cf]
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Code
Pass log file name to Python plugin tools.
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Keith Jolley
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[4974fc]
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Code
Pass user guid to Python plugin to access prefs.
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Keith Jolley
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[4df7fd]
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Code
Version 1.47.3
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Keith Jolley
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[2a4b0f]
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Code
Update 'exact' arg before printing tag sequence box.
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Keith Jolley
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[01c800]
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Code
README and version change not committed.
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Keith Jolley
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[f6768d]
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Code
Run Python offline jobs.
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Keith Jolley
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[f0b293]
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Code
Show Python plugin output on JobViewer.
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Keith Jolley
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[6d2d21]
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Code
CGI.pm encodes multivalue params as a \u0000 separated string.
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Keith Jolley
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[a77df9]
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Code
Merge branch 'develop' into 202407_python_plugins
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Keith Jolley
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[fe7ce9]
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Code
Typo.
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Keith Jolley
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[ea083a]
on
Code
Display correct primary key when only one scheme available.
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Keith Jolley
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[d4f2d7]
on
Code
Set curate option for Python plugin.
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Keith Jolley
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[85636a]
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Code
Pass CGI params to Python plugin.
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Keith Jolley
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[cf9aa1]
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Code
Merge branch 'develop' into 202407_python_plugins
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Keith Jolley
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[7de25c]
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Code
Version 1.47.1.
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Keith Jolley
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[b9e4b7]
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Code
Load Javascript required for Python plugins.
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Keith Jolley
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[01de04]
on
Code
Allow plugin with 'info' section to appear in appropriate menu item.
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Keith Jolley
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[4860e0]
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Code
Remove debugging message.
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Keith Jolley
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[eb848f]
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Code
Don't show plugin buttons on curator tableQuery page.
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Keith Jolley
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[d0081d]
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Code
Add horizontal scroll to allele submissions table.
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Keith Jolley
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[9b3708]
on
Code
Remove obsolete line.
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Keith Jolley
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[e9b259]
on
Code
Respect seqbin_downloads_require_login for EMBL download page.
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Keith Jolley
committed
[1c6c57]
on
Code
Improved accounting for gaps in detecting mutation position.
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Keith Jolley
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[11ece9]
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Code
Projects can now have quotas.
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Keith Jolley
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[3dbec0]
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Code
Allow basic formatting in kiosk text.
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Keith Jolley
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[63c18f]
on
Code
Only return 1000 results in BLAST query if searching single locus.
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Keith Jolley
committed
[b9c00d]
on
Code
Optimize project isolate count query.
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Keith Jolley
committed
[f9cbf1]
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Code
No need to slurp whole file.