#!/usr/bin/env icarus
# BCCM/LMG Bacteria Catalogue - Syntax file
#
# Version 2004.12.17.01
# Last Updated December 17, 2004
# Author: Domenico Marra & Francesca Piersigilli & Paolo Romano
# (c) CABRI 1999-2023
$fn={
Strain_number:strain_no
Name:name
Infrasubspecific_names:inf_name
Organism_type:org_type
Other_collection_numbers:other_nos
Status:status
History:history
Isolated_from:isol_from
Geographic_origin:geo_origin
Conditions_for_growth:cond
Form_of_supply:supply
Serovar:serovar
Mutant:mutant
Genotype:genotype
Remarks:remarks
Applications:apps
Restrictions:rest
Other_names:other_names
}
$rules={
entry: ~ {$In:[file:text] $Out pre $Skip:0}
('Strain_number' {$Not} ln)*
('Strain_number' {$entryFip=$Fip $Wrt} ln {$App}
('Strain_number' {$Not} ln {$App})*)?
~
# fields
fields: ~ {$In:entry $Out $Skip:1}
(/\/[^\n]+\n/ {$Wrt} |
word {$Wrt:$fn.$Ct}
(/[\/A-Z]/ {$Not} ln {$App})+)+
~
# indexing
strain_no: ~ {$In:[fields c:strain_no] $Out}
word ' ' (word2{$Wrt} |punct2)* ~
concat2: ~ {$In:[fields c:name] $Out}
/[^\n]+/ {$Wrt} '\n' (/[^\n]+/ {$App} '\n')* ~
name: ~ {$In:concat2 $Out}
word / /? (word2{$Wrt:[s:$StrRep:[s:$Ct r:"[\"|\.]" to:""]]}
| punct)* ~
rest: ~ {$In:[fields c:rest] $Out}
word / /? (number {$Wrt} | simpleword | punct)* ~
strX: ~ {$In:[fields c:{inf_name org_type status history isol_from
geo_origin cond supply serovar mutant
genotype remarks apps}] $Out}
word (word{$Uniq:$Itc}| /./ |punct)* ~
other_nos: ~ {$In:[fields c:other_nos] $Out}
word / /? (word2{$Uniq} | /;/)* ~
concat: ~ {$In:[fields c:other_names] $Out}
/[^\n]+/ {$Wrt} '\n' (/[^\n]+/ {$App} '\n')* ~
other_names: ~ {$In:concat $Out}
word / /?
(/;/? / /? word2{$Wrt:[ s:$StrRep:[s:$Ct r:"[\"|\.]" to:""]]}
| /,/ /[^;]/+)* ~
namesort: ~ {$In:[fields c:{name}] $Out}
'Name' /[^(\n]+/ {$Wrt} ~
#HTML stuff...
h_top: ~ {$In:[fields c:strain_no t:html] pre if:$ParInt:isTable $Fail}
word {$Rep:
|</TR><TR VALIGN=TOP><TD colspan=2 bgcolor=\"#ffffff\">
|<font color=\"#000066\">
|This entry contains an HTML link to the reference
| database for synonyms of this catalogue.
|If there is no synonym data available, these links
|will be empty.<br><br>
|<B>CABRI:($entry.libName)</B></TD></TR>
|<TR VALIGN=TOP><TD bgcolor=\"#ffffff\"><font color=\"#000066\">
|<b><i>$Ct</i></b></font></TD><TD bgcolor=\"#ffffff\">
}
/.*/ {$Rep:"$Ct</TD></TR>"} ~
h_name: ~ {$In:[fields c:name t:html] pre if:$ParInt:isTable $Fail}
'Name' {if:$isTable==0 $Rep:
|<TR VALIGN=TOP><TD bgcolor=\"#ffffff\"><font color=\"#000066\">
|<b><i> $Ct</i></b></font></TD>
|<TD bgcolor=\"#ffffff\">
} / */
word2 {$rest=$Ct.rep:[' ' to:'%20']
$Rep:$Hlink:[bccm_lmg_namR p:{$rest $Ct}]} ~
h_cond: ~ {$In:[fields c:cond t:html] pre if:$ParInt:isTable $Fail}
'Conditions_for_growth' {if:$isTable==0
$Rep:
|<TR VALIGN=TOP><TD bgcolor=\"#ffffff\">
|<font color=\"#000066\"><b><i>$Ct</i></b>
|</font></TD><TD bgcolor=\"#ffffff\">
}/ */
(simpleword / ?/ number {$rest=$Ct.rep:[' ' to:'%20']
$Rep:$Hlink:[bccm_lmgR p:{$rest $Ct}]}
','? /[^;]/* ';'?)*~
h_rest: ~ {$In:[fields c:rest t:html] pre if:$ParInt:isTable $Fail}
'Restrictions' {if:$isTable==0
$Rep:
|<TR VALIGN=TOP><TD bgcolor=\"#ffffff\">
|<font color=\"#000066\"><b><i>$Ct</i></b></font>
|</TD><TD bgcolor=\"#ffffff\">
}/ */
(simpleword+ number? {$rest=$Ct.rep:[' ' to:'%20']
$Rep:$Hlink:[bccm_lmg_restR p:{$rest $Ct}]})* ~
h_fields: ~ {$In:[fields t:html] pre if:$ParInt:isTable $Fail}
word
{if:$isTable==0 $Rep:
|<TR VALIGN=TOP><TD bgcolor=\"#ffffff\">
|<font color=\"#000066\"><b><i>$Ct</i></b></font>
|</TD><TD bgcolor=\"#ffffff\">
}
/.*/ {$Rep:"$Ct</TD></TR>"} ~
t_fields: ~ {$In:[fields] $Out} tag /.*/ {$Wrt:$Itc} ~
# definitions
tag: ~ word ':'?~
ln: ~ /[^\n]*\n/ ~
word: ~ /[0-9a-zA-Z_]+/ ('/' /[a-zA-Z0-9_]*/)* ~
word2: ~ /[ 0-9a-zA-Z_\/\\.\\+\\%\\*\\(\\)-]+/ ~
punct: ~ /[ \t,;:\.\(\)\+\*-]+/ ~
punct2: ~ /[\t,;:\/\\+]+/ ~
simpleword: ~ /[ a-zA-Z]+/ ~
number: ~ /[0-9]+/ ~
}