#!/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_\/\\.\\+\\%\\*]+/ ~  
}