#!/usr/bin/env icarus
# CBS 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
}
$rules={
entry: ~ {$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)* ~
concat: ~ {$In:[fields c:other_nos] $Out}
/[^\n]+/ {$Wrt} '\n' (/[^\n]+/ {$App} '\n')* ~
name: ~ {$In:[fields c:name] $Out}
word / /? (word2{$Wrt} |punct)* ~
concat2: ~ {$In:[fields c:oth_names] $Out}
/[^\n]+/ {$Wrt} '\n' (/[^\n]+/ {$App} '\n')* ~
oth_names: ~ {$In:concat2 $Out}
word / /?
(/;/? / /? word3 {$Wrt:[s:$StrRep:[s:$Ct r:"[\"|\.]" to:""]]}
| /,/ /[^;]/+)* ~
strX: ~ {$In:[fields c:{name variety org_type restrictions status
history cond substrate origin literature
supply mutant price_code infra isol enzyme
metab applic literature}] $Out}
word (str{$Uniq:$Itc} | /./ | punct)* ~
other_nos: ~ {$In:concat $Out}
word (/ /)* ( '-' | (word2{$Uniq} | /; ?/)* ) ~
#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\">
}
':'? {$Rep:""} /.*/ {$Rep:"$Ct</TD></TR>"} ~
h_cond: ~ {$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\">
}
/ ?/ word4 {$rest=$Ct.rep:[' ' to:'%20']
$Rep:$Hlink:[cbs_bactR p:{$rest $Ct}]}
(',' word4 {$rest=$Ct.rep:[' ' to:'%20']
$Rep:$Hlink:[cbs_bactR p:{$rest $Ct}]})*~
h_name: ~ {$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:[cbs_bact_namR p:{$rest $Ct}]}
| punct) ~
h_fields: ~ {$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_:\\.\\(\\)\/-]+/ ~
str: ~/[a-zA-Z0-9&.'=\/\\%_-]+/ ~
punct: ~ /[ \t,;:\\.\\(\\)\\+\\*]+/ ~
punct2: ~ /[\t,;\/\\+]+/ ~
word3: ~/[ 0-9a-zA-Z_\\"\\.\\(\\)\/\\*-]+/ ~
word4: ~/[ 0-9a-zA-Z_\/\\.\\+\\%\\*]+/ ~
}