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Merge branch '202308_reports' into develop
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@kjolley
kjolley committed Dec 15, 2023
2 parents a75438a + 28d7b86 commit 24ec60d
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Showing 8 changed files with 537 additions and 10 deletions.
5 changes: 4 additions & 1 deletion conf/bigsdb.conf
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Original file line number Diff line number Diff line change
Expand Up @@ -301,10 +301,13 @@ grapetree_limit=10000

#Kleborate########
#Install Kleborate from https://github.com/katholt/Kleborate
#Set location for installation directory 'kleborate_path'.
;kleborate_path=/usr/local/bin/kleborate
;kleborate_record_limit=1000

#weasyprint######
#Only needed for Reports plugin
;weasyprint_path=/usr/bin/weasyprint

#GENEPRESENCE#######
genepresence_taxa_limit=10000
genepresence_record_limit=500000
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6 changes: 4 additions & 2 deletions css/bigsdb.css
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Expand Up @@ -2043,6 +2043,8 @@ div.file_output {
background-image: linear-gradient(#eee, #bce)
}



div#curatetools {
background: #e5e5f0;
float: right;
Expand Down Expand Up @@ -2690,7 +2692,7 @@ span.export_archive {
text-shadow: 3px 3px 3px #999
}

span.export_image {
span.export_image,span.export_html {
color: #47f;
text-shadow: 3px 3px 3px #999
}
Expand All @@ -2700,7 +2702,7 @@ span.export_align {
text-shadow: 3px 3px 3px #999
}

span.export_code {
span.export_code,span.export_pdf {
color: #903;
text-shadow: 3px 3px 3px #999
}
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2 changes: 1 addition & 1 deletion css/bigsdb.min.css
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Binary file added images/plugins/Reports/screenshot.png
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11 changes: 6 additions & 5 deletions lib/BIGSdb/ConfigCheckPage.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -91,7 +91,8 @@ sub _check_helpers {
clustalw => $self->{'config'}->{'clustalw_path'},
ipcress => $self->{'config'}->{'ipcress_path'},
GrapeTree => $self->{'config'}->{'grapetree_path'} . '/grapetree.py',
blat => $self->{'config'}->{'blat_path'}
blat => $self->{'config'}->{'blat_path'},
weasyprint => $self->{'config'}->{'weasyprint_path'}
);
my $td = 1;
say q(<h2>Helper applications</h2>);
Expand Down Expand Up @@ -147,7 +148,7 @@ sub _check_locus_databases {
my $cleaned = $self->clean_locus($locus);
my $locus_db = $self->{'datastore'}->get_locus($locus)->{'db'};
my $buffer =
qq(<tr class="td$td"><td>$cleaned</td><td>$locus_info->{'dbase_name'}</td><td>)
qq(<tr class="td$td"><td>$cleaned</td><td>$locus_info->{'dbase_name'}</td><td>)
. ( $locus_info->{'dbase_host'} // $self->{'system'}->{'host'} )
. q(</td><td>)
. ( $locus_info->{'dbase_port'} // $self->{'system'}->{'port'} )
Expand Down Expand Up @@ -198,7 +199,7 @@ sub _check_scheme_databases {
my ($self) = @_;
say q(<div class="box resultstable">);
say q(<h2>Scheme databases</h2>);
my $set_id = $self->get_set_id;
my $set_id = $self->get_set_id;
my $set_clause = $set_id ? "AND id IN (SELECT scheme_id FROM set_schemes WHERE set_id=$set_id)" : '';
my $schemes =
$self->{'datastore'}->run_query( "SELECT id FROM schemes WHERE dbase_name IS NOT NULL $set_clause ORDER BY id",
Expand Down Expand Up @@ -264,7 +265,7 @@ sub _check_classification_scheme_databases {
my $cscheme_info = $self->{'datastore'}->get_classification_scheme_info($cscheme_id);
my $scheme_info = $self->{'datastore'}->get_scheme_info( $cscheme_info->{'scheme_id'} );
$cscheme_info->{'name'} =~ s/&/&amp;/gx;
$scheme_info->{'name'} =~ s/&/&amp;/gx;
$scheme_info->{'name'} =~ s/&/&amp;/gx;
print qq(<tr class="td$td"><td>$cscheme_info->{'id'}: $cscheme_info->{'name'}</td><td>)
. ("$scheme_info->{'id'}: $scheme_info->{'name'}")
. q(</td><td>)
Expand Down Expand Up @@ -335,7 +336,7 @@ sub _check_client_databases {
my $client = $self->{'datastore'}->get_client_db($_);
my $client_info = $self->{'datastore'}->get_client_db_info($_);
$buffer .=
qq(<tr class="td$td"><td>$client_info->{'name'}</td><td>$client_info->{'description'}</td>)
qq(<tr class="td$td"><td>$client_info->{'name'}</td><td>$client_info->{'description'}</td>)
. qq(<td>$client_info->{'dbase_name'}</td><td>)
. ( $client_info->{'dbase_host'} // $self->{'system'}->{'host'} )
. q(</td><td>)
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10 changes: 9 additions & 1 deletion lib/BIGSdb/Constants.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -172,6 +172,14 @@ use constant ALIGN_FILE => q(<span class="fa-stack fa-2x export">)
use constant CODE_FILE => q(<span class="fa-stack fa-2x export">)
. q(<span class="fas fa-square fa-stack-2x export_code"></span>)
. q(<span class="fas fa-file-code fa-stack-1x fa-inverse"></span></span>);
use constant PDF_FILE => q(<span class="fa-stack fa-2x export">)
. q(<span class="fas fa-square fa-stack-2x export_pdf"></span>)
. q(<span class="fas fa-file-pdf fa-stack-1x fa-inverse"></span></span>);
use constant HTML_FILE => q(<span class="fa-stack fa-2x export">)
. q(<span class="fas fa-square fa-stack-2x export_html"></span>)
. q(<span class="fas fa-file-code fa-stack-1x fa-inverse" style="margin-top:-0.2em"></span>)
. q(<span class="fas fa-stack-text fa-stack-1x" style="font-size:0.4em;)
. q(margin-top:1.5em">HTML</span></span>);
use constant SUBMIT_BUTTON => q(<span class="fa-stack fa-2x upload">)
. q(<span class="fas fa-square fa-stack-2x upload_button"></span>)
. q(<span class="fas fa-upload fa-stack-1x fa-inverse" style="margin-top:-0.2em"></span>)
Expand Down Expand Up @@ -200,7 +208,7 @@ use constant MAX_ROWS => 20;
@values = qw(FACE_STYLE SHOW HIDE SAVE SAVING UP DOWN LEFT RIGHT
EDIT DELETE ADD COMPARE UPLOAD UPLOAD_CHANGE_CONFIG QUERY USERS GOOD BAD MEH TRUE FALSE BAN DOWNLOAD
BACK QUERY_MORE EDIT_MORE UPLOAD_CONTIGS LINK_CONTIGS MORE HOME RELOAD KEY EYE_SHOW EYE_HIDE
CURATE EXPORT_TABLE EXCEL_FILE TEXT_FILE FASTA_FILE FASTA_FLANKING_FILE
CURATE EXPORT_TABLE EXCEL_FILE TEXT_FILE FASTA_FILE FASTA_FLANKING_FILE PDF_FILE HTML_FILE
EMBL_FILE GBK_FILE GFF3_FILE MISC_FILE ARCHIVE_FILE IMAGE_FILE ALIGN_FILE CODE_FILE FLANKING
SUBMIT_BUTTON MAX_ROWS LOCK UNLOCK FIRST PREVIOUS NEXT LAST TOOLTIP WARNING_TOOLTIP);
push @EXPORT_OK, @values;
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1 change: 1 addition & 0 deletions lib/BIGSdb/PluginManager.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -289,6 +289,7 @@ sub _has_required_item {
phyloviz_passwd => 'phyloviz_passwd',
microreact_token => 'microreact_token',
kleborate_path => 'Kleborate',
weasyprint_path => 'weasyprint',
reportree_path => 'ReporTree'
);
return 1 if !$required_attr;
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