error flushing "sock561fc04d8fe0": software caused connection abort
    while executing
"::http::geturl $url"
    (procedure "CheckNewGold" line 4)
    invoked from within
"CheckNewGold"

OUTPUT BUFFER:
source /usr/local/apache2/PourRivet/SessionBeforeScript.tcl
#!/usr/local/bin/tclsh

cd /genomics/link/genomes/gold_genomes


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

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

proc CheckNewGold {} {
    set url "https://gold.jgi.doe.gov/downloadexceldata"
    ::http::register https 443 [list ::tls::socket -tls1 1]
    set tok [::http::geturl $url]
    set goldText [::http::data $tok]
    set gold     [split $goldText \n]
    ::http::cleanup $tok

    set tmd5 [::md5::md5 -hex $gold]
    set omd5 [LesLignesDuFichier gold.md5]

    if {$omd5 eq $tmd5} {
	# same md5, just return
	return 0
    }

    # save new md5
    set o [open gold.md5 w]
    puts $o $tmd5
    close $o
    
    # save native gold data
    file delete gold.txt
    set o [open gold.txt w]
    puts $o $goldText
    close $o
    
    return $gold
}


proc CreateDatabase {Ll} {
    # write data to be inserted 
    if {[file exists ins.tab]} {
	file delete ins.tab
    }
    set o [open ins.tab w]
    foreach l $Ll {
	puts $o "-\t[string map {"'" "''"} [join $l \t]]"
    }
    close $o

    # delete existing database
    if {[file exists gold_genomes.sql]} {
	file delete gold_genomes.sql
    }
    
    # create table
    #
    # 2017/12/15 :
    # GOLDSTAMP | LEGACY GOLDSTAMP | PROJECT NAME | NCBI PROJECT NAME | NCBI BIOPROJECT ACCESSION | NCBI BIOSAMPLE ACCESSION | PROJECT TYPE | PROJECT STATUS | SEQUENCING STATUS | SEQUENCING CENTERS | FUNDING | CONTACT NAME | NCBI TAXON ID | DOMAIN | KINGDOM | PHYLUM | CLASS | ORDER | FAMILY | GENUS | SPECIES | ASSEMBLY ACCESSION | GENBANK

    set table "
        - genomes : gold table {
            . pk_gold P
            . Goldid V16
            . LegalGoldid V16
            . Name V128
            . NCBIProjectName V128
            . NCBIBioProjectAcc V128
            . NCBIBioSampleAcc V128
            . ProjectType V128
            . ProjStatus V64
            . SeqStatus V32
            . Center V128
            . Funding V128
            . Contact V128
            . taxid I
            . Domain V32
            . Kingdom V32
            . Phylum V32
            . Classe V32
            . Ordrr V32
            . Family V32
            . Genus V32
            . Species V32
            . AssemblyAcc V128
            . GenBank V128
         }"
    
    set db [FabriqueDeTables $table "" gold_genomes.sql]
    $db copy abort genomes ins.tab "\t" "-"

    $db eval {create index idx_genomes_taxid on genomes (taxid)}
    $db eval {create index idx_genomes_name on genomes (Name)}
    $db eval {create index idx_genomes_projs on genomes (ProjStatus)}
    $db eval {create index idx_genomes_seqs on genomes (SeqStatus)}
    $db close

    return
}


proc ProcessGold {Ll} {
    set Lins [list]
    # first line is declarations
    # lines end with a \t that should be removed
    # last line is date of last update
    foreach l [lrange $Ll 1 end] {
	if {[string trim $l] eq "" || [string index $l 0] eq "#" || [regexp {^Last run} $l]} {
	    continue
	}
	set Lv [split $l \t]
	lappend Lins [lrange $Lv 0 end-1]
    }

    return $Lins
}

set Lins [list]
if {[set out [CheckNewGold]] != 0} {
    set Lins [ProcessGold $out]
}
if {$Lins != {} } {
    CreateDatabase $Lins
}

exit