#!/usr/bin/env icarus
# DSMZ Human And Animal Cell Lines 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={
Cell_line_name:cell_name
Accession_number:acc_no
Brief_description:brief
Description:description
Morphology:morphology
Culture_conditions:cult_cond
Viruses:viruses
Storage:storage
Properties:properties
Release_conditions:release
Doubling_time:double
Hazard:hazard
Depositor:depositor
Mycoplasma:myco
Bibliographic_reference:refs
Fingerprint:fingerprint
Cytogenetics:cyto
}
$rules={
entry: ~ {$In:[file:text] $Out pre $Skip:0}
('Accession_number' {$Not} ln)*
('Accession_number' {$entryFip=$Fip $Wrt} ln {$App}
('Accession_number' {$Not} ln {$App})*)?
~
# fields
fields: ~ {$In:entry $Out $Skip:1}
(/\/[^\n]+\n/ {$Wrt} |
word {$Wrt:$fn.$Ct}
(/[\/A-Z]/ {$Not} ln {$App})+)+ ~
#indexing
acc_no: ~ {$In:[fields c:acc_no] $Out}
word ' ' (word2{$Wrt} | punct4)* ~
cyto: ~ {$In:[fields c:cyto] $Out}
word (word3{$Wrt} |/./ | punct3)* ~
viruses: ~ {$In:[fields c:viruses] $Out}
word (word3{$Wrt} | /./ | punct2)* ~
cell_name: ~ {$In:[fields c:cell_name] $Out}
word (word { $Wrt:[s:$StrRep:[s:$Ct r:"[\/|\.|-]" to:""]] }
| /./ | punct)* ~
wordX: ~ {$In:[fields c:{cellname brief description storage depositor
refs morphology double myco
fingerprint}] $Out}
word (word{$Uniq:$Itc} | /./ |punct)* ~
strX: ~ {$In:[fields c:{cult_cond properties}] $Out}
word (str{$Uniq:$Itc} | /./ |punct2)* ~
release: ~ {$In:[fields c:release] $Out}
word / / (word2{$Wrt} | punct2) ~
hazard: ~ {$In:[fields c:hazard] $Out}
word / / (number{$Wrt} | /./) ~
#HTML stuff
h_top: ~ {$In:[fields c:acc_no t:html] pre if:$ParInt:isTable $Fail}
word {$Rep:
|</TR><TR VALIGN=TOP>
|<TD colspan=2 bgcolor=\"#ffffff\">
|<font color=\"#000066\">
|<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:"$Ct</TD></TR>"} ~
h_release: ~ {$In:[fields c:release t:html] $Skip:1 pre if:$ParInt:isTable $Fail}
'Release_conditions' {if:$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:[dsmz_mutz_resR p:{$rest $Ct}]})~
h_hazard: ~ {$In:[fields c:hazard t:html] $Skip:1 pre if:$ParInt:isTable $Fail}
'Hazard' {if:$isTable==0
$Rep:
|<TR VALIGN=TOP><TD bgcolor=\"#ffffff\">
|<font color=\"#000066\"><b><i> $Ct</i></b></font></TD>
|<TD bgcolor=\"#ffffff\">
}
/ /? ('-'|
number {$Rep:$Hlink:[dsmz_mutz_hazR p:$Ct]})~
h_fields: ~ {$In:[fields xc:refs t:html] pre if:$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:"$Ct</TD></TR>"} ~
h_biblio_ref: ~ {$In:[fields c:refs t:html]
pre if:$ParInt:isTable $Fail}
bib_tag {if:$isTable==0 $Rep:
|<TR VALIGN=TOP><TD bgcolor=\"#ffffff\">
|<font color=\"#000066\">
|<b><i>$Ct</i></b></font></TD>
|<TD bgcolor=\"#ffffff\">
}
/[^\\[]*/
('[PMID: ' pmid {$Rep:$Hlink:[pubmedCabriR p:{$Ct $Ct}]} ']')?
x{$Rep:"</TD></TR>"} ~
t_fields: ~ {$In:[fields] $Out} tag /.*/ {$Wrt:$Itc} ~
# definitions
tag: ~ word ':'? ~
bib_tag: ~ ('Bibliographic_reference'|'Further_bibliography') ~
bib_word: ~ /[a-zA-Z]+/ ~
bib_vol: ~ (number bib_punct?)+ ~
bib_punct: ~ /[;:.-]/ ~
pmid: ~ /[0-9]+/ ~
ln: ~/[^\n]*\n/ ~
word: ~/[0-9a-zA-Z_\\.\\?\/-]+/ ~
word2: ~/[ 0-9a-zA-Z_\\.\\?\/-]+/ ~
word3: ~/[0-9a-zA-Z_;:\\.\\?\/\\+\\(\\)\\%<>-]+/ ~
punct: ~ /[ \t,;:\\(\\)\\.\\+\\*]+/ ~
punct2: ~ /[ \t,:]+/ ~
punct3: ~ /[ \t,]+/ ~
punct4: ~ /[\t,:]+/ ~
str: ~/[a-zA-Z0-9&.;'=\/\\?\\(\\)\\+\\%_-]+/ ~
number: ~ /[0-9]+/ ~
}