Tuesday, 21 May 2024 13:56:37
Problem unzipping loaded file ...
Msg : stream error
<PRE>
<HR>wrong # args: should be "exit code"
    while executing
"exit"
    (procedure "CheckNewTaxonomy" line 7)
    invoked from within
"CheckNewTaxonomy"<HR>
<P><B>OUTPUT BUFFER:</B></P>
source /usr/local/apache2/PourRivet/SessionBeforeScript.tcl
#!/usr/local/bin/tclsh

cd /genomics/link/taxonomy/uniprot_taxonomy

proc UploadNewTaxonomy {LLignes} {
    global TaxSystem db LGoldId TaxRoot Tx
    
    # Taxon | Mnemonic | Scientific name | Common name | Synonym | Other Names | Reviewed | Rank | Lineage | Parent
    # Check if first line is a header
    if {[string range [lindex $LLignes 0] 0 4] eq "Taxon"} {
	set LLignes [lrange $LLignes 1 end]
    }

    # Then parse file
    set nNodes -1
    foreach Ligne $LLignes {
	if {! ([incr nNodes] % 10000)} {
	    puts "$nNodes done ..."
	}
	if {[string trim $Ligne] eq ""} {continue}

	
	lassign [split $Ligne "\t"] TaxId Mnemonic Name CommonName Synonym OtherNames Reviewed Rank Lineage Parent vir

	set Name       [string map {"'" "''"} $Name]
	set CommonName [string map {"'" "''"} $CommonName]
	set Synonym    [string map {"'" "''"} $Synonym]
	set OtherNames [string map {"'" "''"} $OtherNames]
	set Lineage    [string map {"'" "''"} $Lineage]

	# taxa vides
	if {$Name eq "" && $Parent eq "" && $Lineage eq ""} {
	    continue
	}

	# other sequences
	if {$TaxId == 28384} {
	    set Parent 0
	}

	if {[string trim $Rank] eq ""} {
	    set Rank "no rank"
	}

	# root
	if {[string trim $Name] eq "cellular organisms"} {
	    puts "    ==> root $TaxId"
	    set TaxRoot $TaxId
	    set Parent 0
	}

	if {$Parent eq ""} {
	    set Parent -1
	    puts "Parent -1 : $Name"
	}

	if {! [info exists Name2Tax($TaxId)]} {
	    set Name2Tax($Name) $TaxId
	} else {
	    puts "Warning ! $TaxId existe deja"
	}

	lappend LToInsert [join [list $TaxId $Mnemonic $Name $CommonName $Synonym $OtherNames $Rank $Lineage $Parent $vir] \t]
    }
    puts "reading done ! [llength $LToInsert] entries "
    puts "[DonneDateEtHeure]"
    
    # update ...
    file delete ins.tab
    set o [open ins.tab w]
    puts $o [join $LToInsert \n]
    close $o

    $db eval {PRAGMA synchronous=OFF}
    $db eval {PRAGMA journal_mode = OFF}
    $db copy abort taxonomy ins.tab "\t"
    $db eval {create index idx_taxonomy on taxonomy (taxid, Name, Rank, Parent)}
    $db eval {create index idx_taxonomy_parent on taxonomy (Parent)}
    $db eval {create index idx_taxonomy_rank on taxonomy (Rank)}
    
    puts "\nInsertions done ..."

    return
}


proc InitTable {} {
    set table "
    - taxonomy : {
        . taxid P
        . Mnemonic V32
        . Name V32
        . CommonName V32
        . Synonymous V32
        . OtherNames V32
        . Rank V32
        . Lineage T
        . Parent I
        . virus V32
    }"
    set db [FabriqueDeTables $table "" uniprot_taxonomy.sql]

    return $db
}


proc CheckNewTaxonomy {} {
    set url "http://www.uniprot.org/taxonomy/?format=tab&compress=yes"
    set taxoGZ [HttpCopy $url]
    if {[catch {set taxoText [zlib gunzip $taxoGZ]} Msg]} {
	puts "Problem unzipping loaded file ..."
	puts "Msg : $Msg"
	exit
    }
    set taxo     [split $taxoText \n]
    set tmd5 [::md5::md5 -hex $taxo]
    set omd5 [LesLignesDuFichier uniprot.md5]

    if {$omd5 eq $tmd5} {
	return ""
    }

    # save new md5    
    file delete uniprot.md5
    set o [open uniprot.md5 w]
    puts $o $tmd5
    close $o
    
    # save raw data
    file delete taxonomy.txt
    set o [open taxonomy.txt w]
    puts $o $taxoText
    close $o
    
    return $taxo
}


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
package require tdom

puts "\n[DonneDateEtHeure]"

if {! [file exists uniprot.md5]} {
    set o [open uniprot.md5 w]
    puts $o "FIRSTTIME"
    close $o
}

if {[set out [CheckNewTaxonomy]] != ""} {
    # create new DB
    file delete old_uniprot_taxonomy.sql
    catch {file rename uniprot_taxonomy.sql old_uniprot_taxonomy.sql}
    set db [InitTable]
    UploadNewTaxonomy $out
}

puts "\n[DonneDateEtHeure]"

exit


</PRE>