#!/usr/bin/env icarus
# NCCB 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
Other_collection_numbers:other_nos
Name:name
Infrasubspecific_names:infra
Organism_type:org_type
Restrictions:restrictions
Status:status
History:history
Other_names:oth_names
Isolated_from:isol
Geographic_origin:origin
Mutant:mutant
Enzyme_production:enzyme
Metabolite_production:metab
Applications:applic
Literature:literature
Conditions_for_growth:cond
Form_of_supply:supply
Genotype:genotype
Plasmids:plasmids
Sexual_state:sex_state
Price_code:price_code
}
$rules={
entry: ~ {$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:oth_names] $Out} /[^\n]+/
{$Wrt} '\n' (/[^\n]+/ {$App} '\n')* ~
concat3: ~ {$In:[fields c:name] $Out} /[^\n]+/
{$Wrt} '\n' (/[^\n]+/ {$App} '\n')* ~
name: ~ {$In:concat3 $Out}
'Name ' (word1 {$Wrt:[s:$StrRep:[s:$Ct r:"[\"|\.]" to:""]]}|punct|numero*) ~
oth_names: ~ {$In:concat2 $Out}
word / /? (/;/? / /?
word3{$Wrt:[ s:$StrRep:[s:$Ct r:"[\"|\.]" to:""]]} |
/,/ /[^;]/+)* ~
concat: ~ {$In:[fields c:other_nos] $Out} /[^\n]+/
{$Wrt} '\n' (/[^\n]+/ {$App} '\n')* ~
other_nos: ~ {$In:concat $Out}
word / /? (word2{$Uniq} | /; ?/)* ~
strX: ~ {$In:[fields c:{name infra org_type restrictions status
history oth_names isol origin mutant enzyme
metab applic literature cond supply genotype
plasmids sex_state price_code}] $Out}
word (str{$Uniq:$Itc}| /./ |punct)* ~
# HTML Stuff
h_top: ~ {$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\">
}
/ */ (word1 {$r=$Ct.rep:['.' to: '']
$p=$r.rep:[' ' to:'%20']
$Rep:$Hlink:[nccb_bact_namR p:{$p $Ct}]} | word2 |punct) ~
h_cond: ~ {$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\">
}
(parola numero {$Rep:$Hlink:[nccb_bact_mediumR p:{$Ct $Ct}]}
','? /[^;]/* )* ~
h_fields: ~ {$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\">
} ':'? {$Rep:""} /.*/ {$Rep:"$Ct</TD></TR>"} ~
t_fields: ~ {$In:[fields] $Out} tag /.*/ {$Wrt:$Itc} ~
# definitions
tag: ~ word ':'?~
ln: ~ /[^\n]*\n/ ~
word: ~ /[0-9a-zA-Z_\/]+/ ~
word2: ~ /[ 0-9a-zA-Z_:\\.\\(\\)\/-]+/ ~
word1: ~ /[A-Z][a-z]+[ ]*[a-zA-Z]*/ ~
str: ~ /[a-zA-Z0-9&.'=\/\\%_-]+/ ~
punct: ~ /[ \t,;:\\.\\(\\)\\+\\*-]+/ ~
punct2: ~ /[\t,;\/\\+]+/ ~
word3: ~ /[ 0-9a-zA-Z_\\"\\.\\(\\)\/\\*-]+/ ~
parola: ~ /[^0-9]+/ ~
numero: ~ /[0-9]+/ ~
}