Wednesday, 22 May 2024 02:51:38
<PRE>
<HR>couldn't open "taxdump.tar.gz.md5": permission denied
    while executing
"open taxdump.tar.gz.md5 w"
    (procedure "CheckMD5" line 11)
    invoked from within
"CheckMD5"<HR>
<P><B>OUTPUT BUFFER:</B></P>
source /usr/local/apache2/PourRivet/SessionBeforeScript.tcl
#!/usr/local/bin/tclsh

cd /genomics/link/taxonomy/ncbi_taxonomy

set ORDALIDIR /home/moumou/ordali
set OrdaliDir $ORDALIDIR
source /home/moumou/ordali/src/ordali_source.tcl
source /home/ripp/gscope/gscope_outils.tcl
package require http
package require tls
package require sqlite3
package require md5

proc InitTable {} {
    set table "
        - nodes : {
           . taxid P
           . parent I
           . rank V32
           . embl V2
           . divisionid I
           . inherited_div_flag I (0 ou 1)
           . genetic_code I
           . inherited_GC I
           . mitochondrial_GC I
           . inherited_MGC I
           . genbank_hidden_flag I (0 or 1)
           . hidden_subtree_flag I
           . comments V32
        }
        - names : {
           . pk_names P
           . taxid I
           . name V256
           . unique_name V128
           . name_class V64
        }
        - division : {
           . divisionid I
           . division_code V3
           . division_name V32
           . comments V64
        }
        - gencode : {
           . genetic_code_id I
           . abbreviation I
           . name V128
           . cde V128
           . starts V128
        }
        - citations : {
           . cit_id I
           . cit_key V256
           . pubmid_id I
           . medline_id I
           . url T
           . text T
           . taxid_list T
        }
        - merged : {
           . old I
           . new I
        }
        - delnodes : {
           . delid I
        }"
    
    # cleaning ....
    file rename -force ncbi_taxonomy.sql old_ncbi_taxonomy.sql
    file delete *.dat
    puts "deletion done"

    # create db
    set db [FabriqueDeTables $table "" ncbi_taxonomy.sql]
    puts "db created"

    # expand archive
    exec tar -zxf taxdump.tar.gz
    puts "un-tar done"

    # load db ...
    set Ldmp [glob *.dmp]
    foreach f $Ldmp {
	puts "\n$f"
	#set Ll [LesLignesDuFichier $f]
	set cont [ContenuDuFichier $f]
	set cont [string map {"\t\|\n" "LuCkYlUc67"} $cont]
	set cont [string map {"\n" " "} $cont]
	set cont [string map {"LuCkYlUc67" "  \n"} $cont]
	set Ll [split $cont \n]
	set ofile "[file rootname $f].dat"
	set o [open $ofile w]
	if {[file rootname $f] eq "names"} {
	    set add "\t|\t"
	} else {
	    set add ""
	}
	foreach l $Ll {
	    puts $o "$add[string range $l 0 end-2]"
	}
	close $o
	
	# insert into db
	$db copy abort "[file rootname $f]" "[file rootname $f].dat" "\t\|\t" ""
    }
    $db eval {create index idx_nodes on nodes (parent,rank)}
    $db eval {create index idx_names on names (taxid,name,unique_name)}
    
    $db close

    return
}


proc CheckMD5 {} {
    set url "http://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz.md5"
    set tmd5 [HttpCopy $url]
    set omd5 [ContenuDuFichier taxdump.tar.gz.md5]
    
    if {$tmd5 eq $omd5} {
	return 0
    }

    # save current md5
    set o [open taxdump.tar.gz.md5 w]
    puts $o $tmd5
    close $o

    # now load new archive
    file delete taxdump.tar*
    set url "http://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz"
    set url "ftp://ftp.ncbi.nih.gov/pub/"
    #set tgz [::http::geturl $url -binary 1]
    #set tgz [HttpCopy $url]
    package require ftp
    set url "ftp.ncbi.nih.gov"
    set hdl [::ftp::Open $url "anonymous" "luc.moulinier@unistra.fr"]
    puts "pwd [::ftp::Pwd $hdl]"
    ::ftp::Cd $hdl "pub/taxonomy"
    puts "cd done"
    ::ftp::Type $hdl binary
    puts "binary done"
    ::ftp::Get $hdl "taxdump.tar.gz"
    puts "get file done .."
    ::ftp::Close $hdl
    puts "close done"

    if {0} {
	#set tgz [zlib decompress $tgz]
	set o [open taxdump.tar w]
	puts $o $tgz
	close $o	
    }

    return 1
}
   
puts "\n[DonneDateEtHeure]"
if {[CheckMD5]} {
    InitTable
}
puts "\n[DonneDateEtHeure]"

exit





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