Activity for BIGSdb

  • Keith Jolley committed [f9ecaa] on Code

    Version 1.48.4.

  • Keith Jolley committed [3ca026] on Code

    Collapse multiple coincident cgSTs in isolate results table

  • Keith Jolley committed [9852be] on Code

    Use scheme cache for main results table if large scheme.

  • Keith Jolley committed [ff0cf8] on Code

    Support array fields as identifier fields in seqbin uploads.

  • Keith Jolley committed [952d24] on Code

    Add message about registering account on failed login.

  • Keith Jolley committed [7fee8e] on Code

    Fix hyperlink.

  • Keith Jolley committed [245e0a] on Code

    Version 1.48.3.

  • Keith Jolley committed [a9b744] on Code

    Add space after comma in list of field values to allow wrapping.

  • Keith Jolley committed [05d076] on Code

    Prevent unitialized variable warning.

  • Keith Jolley committed [93875b] on Code

    Scheme.pm doesn't know about its instance.

  • Keith Jolley committed [9d826f] on Code

    Initiate $self->{'system'}->{'script_name'}.

  • Keith Jolley committed [50302b] on Code

    Don't return 'best' match if there zero matches.

  • Keith Jolley committed [14d333] on Code

    Cache closest matching profile by scheme.

  • Keith Jolley committed [dd6663] on Code

    Return empty string if LIN codes not defined.

  • Keith Jolley committed [1ff77e] on Code

    Merge branch '202410_lincode' into develop

  • Keith Jolley committed [4e4c80] on Code

    Slightly more efficient to short-cut out at top of loop.

  • Keith Jolley committed [1354dd] on Code

    Faster calculation of shortest allele.

  • Keith Jolley committed [d85947] on Code

    Get all allele flags and cache if calling multiple times.

  • Keith Jolley committed [bd7e39] on Code

    Cache client fields.

  • Keith Jolley committed [573398] on Code

    Cache locus attribute field lookup.

  • Keith Jolley committed [f4fb8d] on Code

    Include LIN code nicknames on for matching prefixes in seq query.

  • Keith Jolley committed [2cfe5a] on Code

    Include LIN code nicknames on isolate info page.

  • Keith Jolley committed [048e74] on Code

    Use Pg COPY to create BLAST db FASTA.

  • Keith Jolley committed [5a0e13] on Code

    Refactor SequenceQuery::_get_lincode_classification()

  • Keith Jolley committed [9e0769] on Code

    Get partial LIN code in sequence query.

  • Keith Jolley committed [aee776] on Code

    Merge branch 'develop' into 202409_sequence_query

  • Keith Jolley committed [515c52] on Code

    No need to find closest match if we have already found an exact match

  • Keith Jolley committed [766491] on Code

    Set max e-value to 0.001.

  • Keith Jolley committed [f03953] on Code

    Merge branch 'develop' into 202409_sequence_query

  • Keith Jolley committed [b1b5f7] on Code

    Remove obsolete logging.

  • Keith Jolley committed [77de3d] on Code

    Don't use locus common name in sequence query.

  • Keith Jolley committed [b159f5] on Code

    Use Pg COPY to extract profiles from database.

  • Keith Jolley committed [c889bc] on Code

    Show embargo message for normal users.

  • Keith Jolley committed [e236a9] on Code

    Fix date restriction on profile query and viewing profile info page.

  • Keith Jolley committed [ffecac] on Code

    Remove Genbank accession option on sequence query and seqbin upload.

  • Keith Jolley committed [e2b52a] on Code

    Typo.

  • Keith Jolley committed [e9d506] on Code

    Use JQuery.multiselect for merge/update user dropdown boxes.

  • Keith Jolley committed [c5d0ca] on Code

    Add restricted view message on isolate query page

  • Keith Jolley committed [879fdb] on Code

    Allow override of optlist values using field.overrides file.

  • Keith Jolley committed [9dc189] on Code

    Make sure hidden fields are included when creating new version.

  • Keith Jolley committed [57b7ae] on Code

    login_to_show_after_date set in config.xml takes pref over global.

  • Keith Jolley committed [619f4d] on Code

    Remove newline.

  • Keith Jolley committed [75b2ac] on Code

    Use Pg COPY to create cache.

  • Keith Jolley committed [ef6052] on Code

    Mark profile cache stale on automated profile definitions.

  • Keith Jolley committed [a21fda] on Code

    Mark profile cache if profile added, deleted, or updated.

  • Keith Jolley committed [ee5459] on Code

    Cache profiles to file.

  • Keith Jolley committed [242467] on Code

    Version 1.48.2.

  • Keith Jolley committed [0999ad] on Code

    REST: Check scheme has PK before running profiles_csv method.

  • Keith Jolley committed [74f99f] on Code

    Query to filter profiles on number of mismatches is too slow.

  • Keith Jolley committed [58cdf2] on Code

    Merge branch '202409_sequence_query' into 202409_plpgsql

  • Keith Jolley committed [00d3ce] on Code

    Use || as FASTA header separator to allow | in allele identifiers.

  • Keith Jolley committed [8500c6] on Code

    Increased BLASTN word size to 20 (from 15).

  • Keith Jolley committed [1a13fb] on Code

    Use allele length from FASTA header in exact match parse.

  • Keith Jolley committed [5a3c79] on Code

    Save allele length in FASTA header used to create BLAST db

  • Keith Jolley committed [8ed6a6] on Code

    Only check top 20 hits per match length. Check DNA/RNA together.

  • Keith Jolley committed [6e644f] on Code

    Cache seq type determination. Use tr/ rather than s/ to remove spaces

  • Keith Jolley committed [caeb7f] on Code

    Cache allele lookups.

  • Keith Jolley committed [490860] on Code

    Test plpgsql method alongside existing Perl code.

  • Keith Jolley committed [b5773f] on Code

    plpgsql function to lookup profiles.

  • Keith Jolley committed [1c4e8d] on Code

    Version 1.48.1.

  • Keith Jolley committed [19c8be] on Code

    Use offset and limit when building profile list.

  • Keith Jolley committed [e034dc] on Code

    Explicitly use table name when selecting lincodes.profile_id.

  • Keith Jolley committed [5c9c40] on Code

    Fix LIN code prefix lookup on profile info and REST profile pages.

  • Keith Jolley committed [f77407] on Code

    Version 1.48.0.

  • Keith Jolley committed [66e464] on Code

    Remove logging.

  • Keith Jolley committed [833103] on Code

    Fix empty method body when no placeholders defined.

  • Keith Jolley committed [222dd9] on Code

    Merge branch '202409_placeholders' into develop

  • Keith Jolley committed [559a59] on Code

    Optional placeholder text for scheme/LINcode fields.

  • Keith Jolley committed [50a029] on Code

    Add optional placeholder text for provenance and eav fields.

  • Keith Jolley committed [be0150] on Code

    Add comment to bigsdb.conf about virtual environment.

  • Keith Jolley committed [70e297] on Code

    Need full path to grapetree.

  • Keith Jolley committed [0e6ed7] on Code

    Make GrapeTree path consistent with other Python tools.

  • Keith Jolley committed [7175cf] on Code

    Pass log file name to Python plugin tools.

  • Keith Jolley committed [4974fc] on Code

    Pass user guid to Python plugin to access prefs.

  • Keith Jolley committed [4df7fd] on Code

    Version 1.47.3

  • Keith Jolley committed [2a4b0f] on Code

    Update 'exact' arg before printing tag sequence box.

  • Keith Jolley committed [01c800] on Code

    README and version change not committed.

  • Keith Jolley committed [f6768d] on Code

    Run Python offline jobs.

  • Keith Jolley committed [f0b293] on Code

    Show Python plugin output on JobViewer.

  • Keith Jolley committed [6d2d21] on Code

    CGI.pm encodes multivalue params as a \u0000 separated string.

  • Keith Jolley committed [a77df9] on Code

    Merge branch 'develop' into 202407_python_plugins

  • Keith Jolley committed [fe7ce9] on Code

    Typo.

  • Keith Jolley committed [ea083a] on Code

    Display correct primary key when only one scheme available.

  • Keith Jolley committed [d4f2d7] on Code

    Set curate option for Python plugin.

  • Keith Jolley committed [85636a] on Code

    Pass CGI params to Python plugin.

  • Keith Jolley committed [cf9aa1] on Code

    Merge branch 'develop' into 202407_python_plugins

  • Keith Jolley committed [7de25c] on Code

    Version 1.47.1.

  • Keith Jolley committed [b9e4b7] on Code

    Load Javascript required for Python plugins.

  • Keith Jolley committed [01de04] on Code

    Allow plugin with 'info' section to appear in appropriate menu item.

  • Keith Jolley committed [4860e0] on Code

    Remove debugging message.

  • Keith Jolley committed [eb848f] on Code

    Don't show plugin buttons on curator tableQuery page.

  • Keith Jolley committed [d0081d] on Code

    Add horizontal scroll to allele submissions table.

  • Keith Jolley committed [9b3708] on Code

    Remove obsolete line.

  • Keith Jolley committed [e9b259] on Code

    Respect seqbin_downloads_require_login for EMBL download page.

  • Keith Jolley committed [1c6c57] on Code

    Improved accounting for gaps in detecting mutation position.

  • Keith Jolley committed [11ece9] on Code

    Projects can now have quotas.

  • Keith Jolley committed [3dbec0] on Code

    Allow basic formatting in kiosk text.

  • Keith Jolley committed [63c18f] on Code

    Only return 1000 results in BLAST query if searching single locus.

  • Keith Jolley committed [b9c00d] on Code

    Optimize project isolate count query.

  • Keith Jolley committed [f9cbf1] on Code

    No need to slurp whole file.

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