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get-gafs.pl
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get-gafs.pl
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#!/usr/bin/perl -w
use strict;
use warnings;
use Data::Dumper;
use Storable;
use DateTime::Format::Strptime;
## CONFIG
my $go_path = '';
my $base_path = '/Users/gwg/';
my $xrf_abbs = $go_path . 'go/doc/GO.xrf_abbs';
my $checks_script = $go_path . 'go/software/utilities/filter-gene-association.pl';
my $path = $go_path.'go/gene-associations/';
my $svn_repo = 'piwi/go/gene-associations/';
my $user = 'aji';
my $submissions;
if ($path =~ /submission/)
{ $submissions++;
}
##
my ($day, $month, $year) = (localtime)[3, 4, 5];
my $today = sprintf("%04d%02d%02d", $year + 1900, $month + 1, $day);
my $saved;
my $verbose = 1;
## get the names of the dbs in this dir
my $db_list = get_dbs_from_dir();
my $prep;
#get_date_rev_info_cvsweb( logfile => 'tair.log.txt', outfile => 'go/gaf-versions/tair/tair_metadata.txt', db => 'tair', save_path => 'go/gaf-versions/tair/' );
#my @todo = qw( PAMGO_Mgrisea PAMGO_Oomycetes PAMGO_Ddadantii PAMGO_Atumefaciens); #jcvi mgi pombase pseudocap reactome rgd sgd sgn tair rgd wb zfin );
my @todo = qw(zfin);
my $all_mdata_file = 'go/gaf-versions/all-metadata.txt';
my $metadata = parse_all_metadata(metadata_file => $all_mdata_file );
commit_monthly_release( metadata => $metadata );
if ($prep)
{
## prepping files
foreach my $db (@todo)
# foreach my $db (@$db_list)
{ ## make sure we have an appropriate directory to save the files
my $save_path = 'go/gaf-versions/' . $db . '/';
if (! -e $save_path)
{ mkdir($save_path);
}
## create a derived directory
my $derived = $save_path . 'derived/';
if (! -e $derived)
{ mkdir($derived);
}
# get_date_rev_info( db => $db, save_path => $save_path ); #, f_name => $f_name );
# get_files_from_cvs( db => $db, save_path => $save_path );
process_directory_files( db => $db, save_path => $save_path, metadata_file => $all_mdata_file );
print STDERR "Finished processing $db\n" if $verbose;
}
}
exit(0);
foreach my $y (2004..2011)
{ foreach my $m qw(01 02 03 04 05 06 07 08 09 10 11 12)
{ print STDERR "Looking at $y$m...\n";
commit_monthly_release( save_path => 'go/gaf-versions/', metadata => $metadata, date => $y.$m );
}
}
my $date_h;
foreach my $db (@$db_list)
{ my @dates = sort keys %{$metadata->{rev_date}{$db}{by_date}};
$metadata->{first}{ $dates[0] }{$db}++;
$metadata->{last}{ $dates[-1]}{$db}++;
foreach (@dates)
{ $date_h->{$_}++;
}
}
## processing existing files
foreach my $db (@$db_list)
{ ## get all file names
my $save_path = 'go/gaf-versions/' . $db . '/';
my $derived = $save_path . "derived/";
## metadata
# $metadata->{rev_date}{$db} = parse_metadata( db => $db, save_path => $save_path );
## get the list of quarterly files for this db
get_quarterly_files( metadata => $metadata, db => $db, derived => $derived );
}
## see which file sets start when.
foreach my $d (sort keys %{$metadata->{first}})
{ print STDERR "$d\n";
foreach (sort keys %{$metadata->{first}{$d}})
{ print STDERR "$_\t" . $metadata->{rev_date}{$_}{by_date}{$d} . "\n";
}
}
print STDERR "\n\n";
my $dbs;
my $stats;
## what's our start date for each project?
foreach my $d (sort keys %{$metadata->{by_date}})
{ if ($metadata->{first}{$d})
{ foreach (keys %{$metadata->{first}{$d}})
{ $dbs->{$_}++;
}
}
if ($metadata->{last}{$d})
{ foreach (keys %{$metadata->{last}{$d}})
{ delete $dbs->{$_};
}
}
my @files = sort values %{$metadata->{by_date}{$d}};
print STDERR "files for $d:\n" . join("\n", @files) . "\n"; #sort values %{$metadata->{by_date}{$d}}) . "\n";
foreach (sort keys %$dbs)
{ if (! $metadata->{by_date}{$d}{$_})
{ print STDERR "MISSING $_\n";
}
}
# print STDERR "\n\n";
$stats = get_stats(metadata => $metadata, date => $d, files => [ @files ], stats => $stats );
print STDERR "Finished processing files for $d\n";
}
## look at the
exit(0);
sub get_obo_files {
foreach my $y (2007..2011)
{ foreach my $m qw(01 02 03 04 05 06 07 08 09 10 11 12)
{ ## cmd
my $cmd = "cvs -q -d :ext:aji\@ext.geneontology.org:/share/go/cvs update -p -D$y$m"."01 go/ontology/gene_ontology_edit.obo > go/ontology-archive/go-$y$m.obo";
`$cmd`;
}
}
}
sub get_dbs_from_dir {
opendir(DIR, $path) or die "can't opendir $path: $!";
my $dbs;
while (defined(my $file = readdir(DIR)))
{ ## check the file name for the db #
if ($file =~ /gene_association\.(.+)\.gz/)
{ push @$dbs, $1;
}
}
closedir(DIR);
return $dbs;
}
sub get_date_rev_info {
my %args = (@_);
my $f_name = 'gene_association.' .$args{db}. '.gz';
## parse the revision/date list
## use cvs log command to find the file history
## log format:
## ^date: (\d{4})-(\d\d)-(\d\d) \d\d:\d\d:\d\d.*?author: .*?; state: Exp; lines: .*?;
## get the log message
my $cmd = "cvs -q -d :ext:aji\@ext.geneontology.org:/share/go/cvs log $path$f_name";
my $text = `$cmd`;
my @date_arr;
# print STDERR "text: $text\n" if $verbose;
my $temp;
while ($text =~ /----------------------------.*?revision (\d.\d+).*?date: (\d{4})-(\d\d)-(\d\d) \d\d:\d\d:\d\d /sg)
{ ## save the revision and date
$temp->{by_date}{ $2.$3 }{ $1 }++;
$temp->{by_rev}{ $1 }{ $2.$3 }++;
}
foreach my $d (keys %{$temp->{by_date}})
{ ## find the revision with the earliest date
## split up the revision into major and minor parts
my @sorted =
map { $_->[0] }
sort { $a->[1] cmp $b->[1] }
# map { [$_, foo($_)] }
map {
my ($maj, $min) = split(/\./, $_, 2);
[ $_, $maj."\0".$min ];
} keys %{$temp->{by_date}{$d}};
# print STDERR "date: $d; sorted: " . join(", ", @sorted) . "\n\n";
## so for date $d, we want to get $sorted[0]
$saved->{$args{db}}{by_date}{$d} = $sorted[0];
$saved->{$args{db}}{by_rev}{ $sorted[0] }{$d}++;
}
# print STDERR "saved by date: " . join("\n", map { "$_: " . join(", ", @{$saved->{by_date}{$_}} ) } sort keys %{$saved->{by_date}}) . "\n\n";
## save this info so we don't have to retrieve it again
open(FH, "> $args{save_path}" . "metadata.txt") or die "Could not create file " . $args{save_path} . "metadata for writing: $!";
print FH "Saved: by date:\n" . join("\n", map { "$_: " . $saved->{$args{db}}{by_date}{$_} } sort keys %{$saved->{$args{db}}{by_date}}) . "\n\n";
print FH "\n\nAll revisions:\n";
foreach my $k (sort keys %{$saved->{$args{db}}{by_rev}})
{ print FH "$k:\n" . join(", ", sort keys %{$saved->{$args{db}}{by_rev}{$k}}) . "\n";
}
close(FH);
}
## work out the metadata from a log copied from a cvsweb page
## note that we put in a line so that the format is
## ----------------------------
## Revision 1.1239: download
## Wed Feb 8 03:16:40 2009 UTC (2 years, 11 months ago) by gocvs
## Branches: MAIN
sub get_date_rev_info_cvsweb {
my %args = (@_);
## parse the revision/date list
## use cvs log command to find the file history
my $temp;
my $parser = DateTime::Format::Strptime->new( pattern => '%b %d %H:%M:%S %Y' );
## log format:
## Revision 1.1239: download
## Wed Feb 8 03:16:40 2009 UTC (2 years, 11 months ago) by gocvs
## get the log message
my $logfile = $args{logfile};
## open it up, let the separator be the line of hyphens
open(LOG, "< $args{logfile}") or die "Could not open $args{logfile}: $!";
{ local $/ = "----------------------------";
while (<LOG>)
{ next unless /\w/;
if (/Revision (\d\.\d+): download\s+\w+ ((Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec) \d{1,2} \d\d:\d\d:\d\d (19|20)\d\d UTC)/)
{ my $rev = $1;
my $date = $2;
## parse the date
my $dt = $parser->parse_datetime( $date );
## convert into YYYYMMDD
$date = $dt->strftime( "%Y%m" );
## save the revision and date
$temp->{by_date}{ $date }{ $rev }++;
$temp->{by_rev}{ $rev }{ $date }++;
}
elsif (/Revision (\d\.\d+)/)
{ warn "Could not parse revision/date: check $_";
}
}
}
foreach my $d (keys %{$temp->{by_date}})
{ ## find the revision with the earliest date
## split up the revision into major and minor parts
my @sorted =
map { $_->[0] }
sort { $a->[1] cmp $b->[1] }
# map { [$_, foo($_)] }
map {
my ($maj, $min) = split(/\./, $_, 2);
[ $_, $maj."\0".$min ];
} keys %{$temp->{by_date}{$d}};
# print STDERR "date: $d; sorted: " . join(", ", @sorted) . "\n\n";
## so for date $d, we want to get $sorted[0]
$saved->{$args{db}}{by_date}{$d} = $sorted[0];
$saved->{$args{db}}{by_rev}{ $sorted[0] }{$d}++;
}
## save this info so we don't have to retrieve it again
open(FH, "> " . $args{outfile}) or die "Could not create file " . $args{outfile} . " for writing: $!";
print FH "Saved: by date:\n" . join("\n", map { "$_: " . $saved->{$args{db}}{by_date}{$_} } sort keys %{$saved->{$args{db}}{by_date}}) . "\n\n";
print FH "\n\nAll revisions:\n";
foreach my $k (sort keys %{$saved->{$args{db}}{by_rev}})
{ print FH "$k:\n" . join(", ", sort keys %{$saved->{$args{db}}{by_rev}{$k}}) . "\n";
}
close(FH);
foreach my $d (keys %{$saved->{$args{db}}{by_date}})
{ ## location for saved file
## date: $d; revision: $saved->{$args{db}}{by_date}{$d}
my $save_file = $args{db}."-r-".$saved->{$args{db}}{by_date}{$d}."-d-".$d.".gaf.gz";
## let's check whether we have this file already!
if (! -e $args{save_path}.$save_file)
{
my $cmd = "cvs -q -d :ext:aji\@ext.geneontology.org:/share/go/cvs update -p -r " . $saved->{$args{db}}{by_date}{$d} . " go/gene-associations/gene_association.tair.Mar2004-Feb2009.gz > $args{save_path}$save_file";
print STDERR "Running $cmd\n" if $verbose;
my $status = `$cmd`;
## check the status?
if ($status =~ /is no longer in the repository/)
{ warn "ERROR: performing update to " . $saved->{$args{db}}{by_date}{$d} . "; error:\n$status";
}
}
}
}
sub get_files_from_cvs {
my %args = (@_);
## get the revisions we're looking for
my $status;
my $f_name = 'gene_association.' .$args{db}. '.gz';
if (! $saved || ! $saved->{$args{db}})
{ $saved->{$args{db}} = parse_metadata(%args);
}
foreach my $d (keys %{$saved->{$args{db}}{by_date}})
{ ## location for saved file
## date: $d; revision: $saved->{$args{db}}{by_date}{$d}
my $save_file = $args{db}."-r-".$saved->{$args{db}}{by_date}{$d}."-d-".$d.".gaf.gz";
## let's check whether we have this file already!
if (! -e $args{save_path}.$save_file)
{
my $cmd = "cvs -q -d :ext:aji\@ext.geneontology.org:/share/go/cvs update -p -r " . $saved->{$args{db}}{by_date}{$d} . " $path$f_name > $args{save_path}$save_file";
print STDERR "Running $cmd\n" if $verbose;
$status = `$cmd`;
## check the status?
if ($status =~ /is no longer in the repository/)
{ warn "ERROR: performing update to " . $saved->{$args{db}}{by_date}{$d} . " of $f_name; error:\n$status";
}
}
}
}
sub process_directory_files {
my %args = (@_);
## now let's go through the files and tidy things up
## get the contents of $args{save_path} and iterate through them
opendir(DIR, $args{save_path}) or die "can't opendir $args{save_path}: $!";
my @to_check;
while (defined(my $file = readdir(DIR)))
{ # do something with "$dirname/$file"
## check the file name for the revision #
if ($file =~ /(.*?)-r-(\d\.\d+)-d-(\d{6}).gaf(.gz)?/)
{ push @to_check, [ $file, $3 ];
# $rev = $1;
}
else
{ #print STDERR "No revision found for $file!\n";
next;
}
}
closedir(DIR);
## make sure that we have the metadata (if reqd)
## find the latest date for this file, remove annots after that date.
if (! $saved || ! $saved->{$args{db}})
{ $saved->{$args{db}} = parse_all_metadata( %args );
}
my @sorted = map { $_->[0] } sort { $a->[1] <=> $b->[1] } @to_check;
my $status;
my @done;
foreach my $file (@sorted)
{ my $rev;
my $date;
my $year;
my $month;
my $date_8;
if ($file =~ /(.*?)-r-(\d\.\d+)-d-(\d{4})(\d{2})/)
{ $rev = $2;
$year = $3;
$month = $4;
}
$date = $year . $month;
my $previous_quarter;
if ($month eq '01')
{ $previous_quarter = $year;
$previous_quarter--;
$previous_quarter .= '1000';
}
elsif ($month eq '04')
{ $previous_quarter = $year . '0100';
}
elsif ($month eq '07')
{ $previous_quarter = $year . '0400';
}
elsif ($month eq '10')
{ $previous_quarter = $year . '0700';
}
## add two zeros to the date to convert it into the eight digit format
$date_8 = $date . "00";
## make sure that the file exists and has a non-zero size
if (! -e $args{save_path}.$file || -z $args{save_path}.$file)
{ print STDERR "$args{save_path}$file does not exist or has zero size!\n";
next;
}
## new files to create
my $sorted = $args{save_path}. "derived/" . $args{db} . "-r-". $rev . "-sorted.gaf";
my $filter = $args{save_path}. "derived/" . $args{db} . "-r-". $rev . "-filter.gaf";
my $recent = $args{save_path}. "derived/" . $args{db} . "-r-". $rev . "-recent.gaf";
next if (-e $sorted || -e $filter);
# print STDERR "Looking at $file; revision: $rev; date: $date\n" if $verbose;
my $n_lines;
if ($previous_quarter)
{ $n_lines = remove_dupes_and_filter_by_date( %args, date_8 => $date_8, file => $file, sorted => $sorted, recent => $recent, previous_quarter => $previous_quarter);
}
else
{ $n_lines = remove_dupes_and_filter_by_date( %args, date_8 => $date_8, file => $file, sorted => $sorted);
}
## $sorted should now contain all unique lines
if (! $n_lines || $n_lines == 0)
{ warn "No body lines found in $file!";
next;
}
if ($submissions)
{ ## if we have the appropriate OBO file, run the GAF filter script
if ($date > 200610)
{ my $error = run_checks_script( %args, date => $date, input => $sorted, output => $filter);
## if it ran OK, let's replace $sorted with $filter
if (! $error)
{ my $status = `mv $filter $sorted`;
if ($status)
{ warn "Error: mv $filter $sorted: $status";
}
}
}
}
}
=cut
## open the annotation file, remove the header lines
open(F, "gzip -dc $args{save_path}$file |") || die "cannot open $args{save_path}$file: $!";
open(HEAD, "> $f_head") or die "Could not open $f_head for writing: $!";
while (<F>)
{ next unless /\w/;
if (/^!/)
{ print HEAD $_;
}
else
{ ## see if we have an annotation line
if (/(.*?\t){10,}/)
{ last;
}
}
}
close(F);
close(HEAD);
## sort the file lines, removing dupes, decompressing if rqd
$status = `gzip -dc $args{save_path}$file | sort -u -o $sorted`;
if ($status)
{ warn "running sort -u; status: $status";
}
## open the sorted file, remove the header lines and extract the annotation data
open(F, "< $sorted") || die "cannot open $sorted: $!";
open(EDIT, "> $f_edit") or die "Could not open $f_edit for writing: $!";
my $count;
## now process this file.
while (<F>)
{ next unless /\w/;
next if /^!/;
## extract the stuff we want
chomp;
my @cols = split /\t/, $_;
my $n_cols = scalar @cols;
while ($n_cols < 17)
{ push @cols, "";
$n_cols++;
}
if ($date_8)
{ ## find the date, check if we're OK or not
next if ! $cols[13]; ## no date specified
next if $cols[13] > $date_8; ## later than our cutoff date
}
## body material!
print BODY $_ . "\n";
$count->{body}++;
print EDIT join("\t", map { "$_" || "" } ($cols[0], $cols[1], "", @cols[3..7],
("", "", "", ""),
@cols[12..$#cols]) ). "\n";
}
close EDIT;
close BODY;
if (! $count->{body} || $count->{body} < 0)
{ print STDERR "No lines found in body of $file!\n";
next;
}
## sort and remove dupes in EDIT
my $cmd = "sort -u -o $e_sort $f_edit";
$status = `$cmd`;
if ($status)
{ warn "running sort -u on edited file: $status";
}
open(FILE, "< $e_sort") or die "can't open $e_sort: $!";
$count->{edit} += tr/\n/\n/ while sysread(FILE, $_, 2 ** 16);
close FILE;
# push @done, $edited_sort;
if ($count->{body} != $count->{edit})
{ warn "$args{db} r $rev diffs: lost " . ($count->{body} - $count->{edit}) . " lines";
}
# gaf_stats($edited_sort);
## put the head and the body of the file back together, save with the new date
$cmd = `cat $f_head $f_body > $f_new`;
$status = `$cmd`;
if ($status)
{ warn "concatenating head and body files: $status";
}
## now run the checks script
## only need to do this on the submissions files
if ($error)
{ ## Don't commit!!
}
else
{ ## we're ready to commit.
# svn_commit_file( %args, date => $date_8, rev => $rev, file => $filter );
}
}
=cut
}
=cut
Remove duplicate lines, filter by date
input: file, f_head, sorted, f_body
output: n lines of body
=cut
sub remove_dupes_and_filter_by_date {
my %args = (@_);
## open the annotation file, remove the header lines
open(F, "gzip -dc $args{save_path}$args{file} |") || die "cannot open $args{save_path}$args{file}: $!";
open(OUT, "> $args{sorted}") or die "Could not open $args{sorted} for writing: $!";
while (<F>)
{ next unless /\w/;
if (/^!/)
{ print OUT $_;
}
else
{ ## see if we have an annotation line
if (/(.*?\t){10,}/)
{ last;
}
}
}
close F;
close OUT;
## sort the file lines, removing dupes, decompressing if rqd
## save the data in a temporary file
my $temp = $args{sorted} . ".temp";
my $status = `gzip -dc $args{save_path}$args{file} | sort -u -o $temp`;
if ($status)
{ warn "running sort -u; status: $status";
}
if ($args{previous_quarter})
{ open(Q, "> $args{recent}") or die "Could not open $args{recent} for writing: $!";
}
## open the sorted file, remove the header lines and extract the annotation data
open(S, "< $temp") || die "cannot open $temp: $!";
open(OUT, ">> $args{sorted}") or die "Could not open $args{sorted} for writing: $!";
my $count = 0;
my $dates;
## now process this file.
while (<S>)
{ next unless /\w/;
next if /^!/;
## extract the stuff we want
chomp;
my @cols = split /\t/, $_;
next if ! $cols[13]; ## no date specified
if ($cols[13] !~ /^\d{8}$/)
{ warn "Incorrect date format in $args{file} line\n$_";
next;
}
if ($args{date_8})
{ ## find the date, check if we're OK or not
$dates->{ $cols[13] }++;
next if $cols[13] > $args{date_8}; ## later than our cutoff date
}
## body material!
print OUT $_ . "\n";
$count++;
if ($args{previous_quarter} && $cols[13] > $args{previous_quarter})
{ print Q $_ . "\n";
}
}
close OUT;
close S;
if ($args{previous_quarter})
{ close Q;
}
print STDERR "file: $args{file}; date: $args{date_8}; previous quarter: ". ( $args{previous_quarter} || "N/A" ) . "\n" . join("\n", map { "$_\t" . $dates->{$_} } sort keys %$dates) . "\n\n";
## delete the temp file
unlink $temp;
return $count;
}
sub run_checks_script {
# return;
my %args = (@_);
# return if $args{date} < 200611;
## the obo file
my $cmd = "$checks_script -i $args{input} -p nocheck -o /Users/gwg/go/ontology-archive/go-".$args{date}.".obo -n ".$args{date}."00 -w 2>&1 1>$args{output}";
print STDERR "running $cmd\n" if $verbose;
my $status = `$cmd`;
if ($status =~ /TOTAL ERRORS or WARNINGS = (\d+)\s.*?TOTAL out of date IEAs removed = (\d+)\s.*?Total of (\d+) lines \(not including header\) written to STDOUT./s)
{ my $total = $3;
my $errs = $1 - $2;
return if $errs == 0;
if ($total == 0)
{ warn "No lines left after checking $args{input}!";
return 1;
}
## ignoring IEAs, how many dodgy lines did we get rid of?
my $ten_percent = $total / 10;
if ($errs > $ten_percent)
{ ## get percentage errors
my $p = sprintf("%.1f", $errs / $total * 100);
warn "$args{input} has error rate $p\%";
return 1;
}
}
elsif ($status =~ /Congratulations, there are no errors/)
{
}
else
{ warn "No report produced by $checks_script! status: $status";
}
}
## move files to cvs sub dirs, create GPX files
sub prep_monthly_release {
my %args = (@_);
## get all the files for that month
if (! $args{metadata})
{ $args{metadata} = parse_all_metadata(%args);
}
if ($args{date})
{ ## find that date in the metadata, work out the names of the files reqd
FILE_CHECK:
foreach my $db (keys %{$metadata->{rev_date}})
{ print STDERR "Looking at $db...\n";
if ($metadata->{rev_date}{$db}{by_date}{$args{date}})
{ ## work out the file name
my $errs;
my $rev = $metadata->{rev_date}{$db}{by_date}{$args{date}};
my $f = $args{save_path} . $db . "/derived/" . $db . "-r-". $rev . "-sorted.gaf";
if (! -e $f)
{ warn "Could not find release file $f!";
$errs++;
next FILE_CHECK;
}
## copy file to the release directory
## new file name
my $new_f_name = "gene_association." . $db . "-r-" . $rev . ".gaf";
my $new_f_dir = $svn_repo . 'gaf/';
my $status = `cp $f $new_f_dir$new_f_name`;
if ($status)
{ warn "Error copying $f: $status";
$errs++;
next FILE_CHECK;
}
if (! $errs)
{ ## check whether we have the files or not:
my $gpad_f = $svn_repo . 'gpad/' . $db . "-r-$rev.gpad";
my $gpi_f = $svn_repo . 'gpi/' . $db . "-r-$rev.gpi";
if (-e $gpad_f && -e $gpi_f)
{ next FILE_CHECK;
}
## create the GPAD/GPI files
my $cmd = 'perl /Users/gwg/obo-scripts/gaf2gpx.pl -i ' . $new_f_dir . $new_f_name
. ' --gpad ' . $svn_repo . 'gpad/' . $db . "-r-$rev.gpad"
. ' --gpi ' . $svn_repo . 'gpi/' . $db . "-r-$rev.gpi";
# . ' -v';
print STDERR "About to GPXify $new_f_name\n";
my $status = `$cmd`;
print STDERR $status . "\n";
}
}
else
{ #warn "No files found for date $args{date}";
}
}
## svn copy svn+ssh://ext.geneontology.org/share/go/svn/trunk/gene-associations svn+ssh://ext.geneontology.org/share/go/svn/releases/YYYY-MM-DD
}
}
sub commit_monthly_release {
my %args = (@_);
## get all the files for that month
if (! $args{metadata})
{ $args{metadata} = parse_all_metadata(%args);
}
my $m_data = $args{metadata};
chdir $svn_repo;
# $meta->{rev_date}{$cols[0]}{by_date}{$cols[1]} = $cols[2];
my $st = `pwd`;
print STDERR $st . "\n\n";
$st = `svn info`;
print STDERR $st . "\n\n";
## find that date in the metadata, work out the names of the files reqd
## index the files by date, not db
foreach my $db (keys %{$m_data->{rev_date}})
{ foreach my $date (keys %{$m_data->{rev_date}{$db}{by_date}})
{ $m_data->{by_date}{$date}{$db} = $m_data->{rev_date}{$db}{by_date}{$date};
}
}
my $path = '/Users/gwg/piwi/';
foreach my $date (sort keys %{$m_data->{by_date}})
{ my $err;
my $status;
foreach my $db (keys %{$m_data->{by_date}{$date}})
{ my $rev = $m_data->{by_date}{$date}{$db};
## copy file to the release directory
## check whether we have the files or not:
my $gaf_f = $path.'gaf/gene_association.' . $db . "-r-" . $rev . ".gaf";
my $gpad_f = $path.'gpad/' . $db . "-r-$rev.gpad";
my $gpi_f = $path.'gpi/' . $db . "-r-$rev.gpi";
my $new_gaf_f = "gaf/gene_association." . $db . ".gaf";
my $new_gpad_f = 'gpad/' . $db . ".gpad";
my $new_gpi_f = 'gpi/' . $db . ".gpi";
if (-e $gpad_f && -e $gpi_f && -e $gaf_f)
{ # OK, we're good to commit!
# copy these files to the 'master' version
my $cmd = "cp $gaf_f $new_gaf_f";
print STDERR "Running $cmd\n";
$status = `$cmd`;
if ($status)
{ warn $status;
$err++;
}
$cmd = "cp $gpi_f $new_gpi_f";
print STDERR "Running $cmd\n";
$status = `$cmd`;
if ($status)
{ warn $status;
$err++;
}
$cmd = "cp $gpad_f $new_gpad_f";
print STDERR "Running $cmd\n";
$status = `$cmd`;
if ($status)
{ warn $status;
$err++;
}
}
else
{ warn "Missing files for $date, $db, $rev:" .
( -e $gpad_f ? "" : " GPAD" )
. (-e $gpi_f ? "" : " GPI" )
. (-e $gaf_f ? "" : " GAF" )
. "\n";
}
}
if ($err)
{ warn "Aborting commit of files for $date";
next;
}
## otherwise, let's commit!
my $cmd = "svn commit --username bbop --password bbop -m 'GAF, GPI, GPAD files for date " . $date . "'";
print STDERR "About to run\n$cmd\n";
$status = `$cmd 2>&1`;
if ($status)
{ warn "svn commit: $status";
}
else
{ warn "svn commit seemed to work!";
}
# exit(0);
## Try making the monthly release
$cmd = "svn copy svn://piwi.lbl.gov/go/gene-associations svn://piwi.lbl.gov/go/releases/".$date."01";
# $status = `$cmd`;
# if ($status)
# { warn "svn copy failed! $status";
## svn copy svn+ssh://ext.geneontology.org/share/go/gene-associations svn+ssh://ext.geneontology.org/share/go/releases/YYYY-MM-DD
# }
}
}
sub svn_commit_file {
my %args = (@_);
## copy the file to the correct directory.
## compress the file??
## new file name is gene-association.DBNAME.gaf
my $f_name = "gene-association.".$args{db}.".gaf";
my $cmd = "cp $args{file} $svn_repo$f_name";
print STDERR "about to run $cmd\n";
my $status = `$cmd`;
if ($status)
{ warn "copy: $status";
}
$user = 'bbop';
## commit this file to svn?
chdir $svn_repo;
$cmd = "svn commit -m 'Gene association file for " . $args{db} . "; release date: " . $args{date} . ", CVS revision: " . $args{rev} . "' $f_name";
print STDERR "About to run\n$cmd\n";
$status = `$cmd`;
if ($status)
{ warn "svn commit: $status";
}
chdir $base_path;
# $cmd = "svn copy svn+ssh://$user\@ext.geneontology.org/share/go/svn/trunk/gene-associations/$args{f_name} svn+ssh://$user\@ext.geneontology.org/share/go/svn/releases/$args{date}";
# $status = `$cmd`;
# if ($status)
# { warn "svn copy to release directory: $status";
# }
}
## input: save_path => ..., db => ...
sub parse_metadata {
my %args = (@_);
my $meta;
## open the metadata file
# sftp://plutonium.lbl.gov//Users/gwg/go/gaf-versions/aspgd/metadata.txt
open( M, "< " . $args{save_path} . 'metadata.txt') or die "Could not open metadata file: " . $args{save_path} . "metadata.txt: $!";
my $on;
while (<M>)
{ next unless /\w/;
last if /All revisions:/;
if (/Saved: by date:/)
{ $on++;
}
elsif ($on)
{ if (/(\d{6}): (\d+\.\d+)/)
{ $meta->{by_date}{$1} = $2;
$meta->{by_rev}{$2} = $1;
}
}
}
close(M);
return $meta;
}
## input: save_path => ..., db => ...
sub parse_all_metadata {
my %args = (@_);
my $meta;
## open the metadata file
open( M, "< " . $args{metadata_file}) or die "Could not open metadata file " . $args{metadata_file} .": $!";
my $on;
while (<M>)
{ next unless /\w/;
chomp;
my @cols = split(/\t/, $_, 3);
$meta->{rev_date}{$cols[0]}{by_date}{$cols[1]} = $cols[2];
$meta->{rev_date}{$cols[0]}{by_rev}{$cols[2]} = $cols[1];
}
close(M);
return $meta;
}
sub get_quarterly_files {
my %args = (@_);
opendir(DIR, $args{derived}) or die "can't opendir $args{derived}: $!";
my $files;
while (defined(my $file = readdir(DIR)))
{ ## check the file name for the db #
if ($file =~ /-r-(\d\.\d+)-recent\.gaf$/)
{ ## find the date from the metadata
if ($metadata->{rev_date}{ $args{db} }{by_rev}{$1})
{ $metadata->{by_date}{ $metadata->{rev_date}{ $args{db} }{by_rev}{$1} }{ $args{db} } = $file;
}
else
{ warn "Could not find date for $file!";
}
$metadata->{by_rev}{$args{db}}{$1} = $file;
}
}
closedir(DIR);
return $files;
}
sub write_metadata {
my $m_file = 'go/gaf-versions/all-metadata.txt';
open(M, "> $m_file") or die "Could not open $m_file: $!";
foreach my $db (sort keys %{$metadata->{rev_date}})
{ foreach my $d (sort keys %{$metadata->{rev_date}{$db}{by_date}})
{ print M "$db\t$d\t" . $metadata->{rev_date}{$db}{by_date}{$d} . "\n";
}
print M "\n";
}
close M;
}
sub get_stats {
my %args = (@_);
## fname of the form
## aspgd/derived/aspgd-r-1.121-recent.gaf
my $quarter = {
'01' => '1',
'02' => '1',
'03' => '1',
'04' => '2',
'05' => '2',
'06' => '2',
'07' => '3',
'08' => '3',
'09' => '3',
'10' => '4',
'11' => '4',
'12' => '4',
};
my $all_stats;
my $q_stats;
my $database;
foreach my $file (@{$args{files}})
{ ## find db name
# print STDERR "looking at $file\n";
if ($file =~ /^(.*?)-r-\d\.\d+/)
{ $database = $1;
}
else
{ warn "Unknown database name: $file";
}
my $file_path = "go/gaf-versions/$database/derived/";
# print STDERR "Looking at $file_path$file for $database\n";
next unless -e $file_path && -e $file_path.$file;
# print STDERR "Found file, about to open it...\n";
if ($file =~ /\.gz$/)
{ open( FH, "gzip -dc $file_path$file|") or die "Could not open $file: $!";
}
else
{ open( FH, "< $file_path$file") or die "Could not open $file: $!";
}
if (! -e 'go/gaf-versions/stats')
{ mkdir 'go/gaf-versions/stats';
}
my $output = "go/gaf-versions/stats/$database-".$args{date}."-stats.txt";
# print STDERR "output going to $output\n";