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Revision 1.12 - (view) (download) (as text)
| 1 : | jared | 1.1 | package MGRASTBackend::MGRASTPipeline; |
| 2 : | |||
| 3 : | use ClusterStage; | ||
| 4 : | use Filesys::DfPortable; | ||
| 5 : | use Mail::Mailer; | ||
| 6 : | use Job48; | ||
| 7 : | use FIG; | ||
| 8 : | |||
| 9 : | use strict; | ||
| 10 : | use warnings; | ||
| 11 : | |||
| 12 : | use base qw( Exporter ); | ||
| 13 : | our @EXPORT = qw ( check_free_space get_jobs get_pipeline_for_job process_upload mark_job_done); | ||
| 14 : | |||
| 15 : | 1; | ||
| 16 : | |||
| 17 : | |||
| 18 : | ######################################## | ||
| 19 : | # | ||
| 20 : | # Basic methods | ||
| 21 : | # | ||
| 22 : | ######################################### | ||
| 23 : | |||
| 24 : | sub check_free_space { | ||
| 25 : | my ($job_spool_dir) = @_; | ||
| 26 : | my $df = dfportable($job_spool_dir, 1024*1024*1024); | ||
| 27 : | if (!defined($df)){ | ||
| 28 : | die "dfportable call failed on $job_spool_dir: $!"; | ||
| 29 : | } | ||
| 30 : | if ($df->{bavail} < 10){ | ||
| 31 : | die sprintf "Not enough free space available (%.1f GB) in $job_spool_dir", $df->{bavail}; | ||
| 32 : | } | ||
| 33 : | return; | ||
| 34 : | } | ||
| 35 : | |||
| 36 : | sub get_jobs { | ||
| 37 : | my ($job_spool_dir) = @_; | ||
| 38 : | opendir(D, $job_spool_dir) or die "Cannot open job directory $job_spool_dir: $!\n"; | ||
| 39 : | my @jobs = sort { $a <=> $b } grep { /^\d+$/ and -d "$job_spool_dir/$_" } readdir(D); | ||
| 40 : | return \@jobs; | ||
| 41 : | } | ||
| 42 : | |||
| 43 : | sub get_pipeline_for_job { | ||
| 44 : | my ($job_dir) = @_; | ||
| 45 : | jared | 1.4 | if(! -f "$job_dir/PIPELINE"){ |
| 46 : | jared | 1.1 | return &{&pipeline("default")}; |
| 47 : | } else { | ||
| 48 : | jared | 1.4 | my $pipe = &FIG::file_head("$job_dir/PIPELINE", 1); |
| 49 : | jared | 1.1 | chomp $pipe; |
| 50 : | if (ref(&pipeline($pipe)) eq 'CODE'){ | ||
| 51 : | return &{&pipeline($pipe)}; | ||
| 52 : | } else { | ||
| 53 : | return undef; | ||
| 54 : | } | ||
| 55 : | } | ||
| 56 : | } | ||
| 57 : | |||
| 58 : | ######################################## | ||
| 59 : | # | ||
| 60 : | # Pipelines | ||
| 61 : | # | ||
| 62 : | ######################################### | ||
| 63 : | |||
| 64 : | sub pipeline { | ||
| 65 : | my ($name) = @_; | ||
| 66 : | my %pipelines = ( | ||
| 67 : | default => \&default_process, | ||
| 68 : | arodri7 | 1.9 | figfams => \&figfam_process, |
| 69 : | jared | 1.1 | ); |
| 70 : | |||
| 71 : | if(defined $pipelines{$name}){ | ||
| 72 : | return $pipelines{$name}; | ||
| 73 : | } else { | ||
| 74 : | jared | 1.7 | return $pipelines{default}; |
| 75 : | jared | 1.1 | } |
| 76 : | } | ||
| 77 : | |||
| 78 : | sub default_process { | ||
| 79 : | return [[uploaded => \&process_upload], | ||
| 80 : | [preprocess => ClusterStage->new('mg_preprocess', | ||
| 81 : | sge_flag => "-l mg_preprocess", | ||
| 82 : | )], | ||
| 83 : | [sims => ClusterStage->new('mg_sims', | ||
| 84 : | start_locally => 1, | ||
| 85 : | )], | ||
| 86 : | [check_sims => ClusterStage->new('mg_check_sims', | ||
| 87 : | start_locally => 1, | ||
| 88 : | )], | ||
| 89 : | [create_seed_org => ClusterStage->new('mg_create_seed_org', | ||
| 90 : | sge_flag => "-l mg_postproc_taxa_sims", | ||
| 91 : | )], | ||
| 92 : | jared | 1.6 | [export_to_genbank => ClusterStage->new('mg_sims_to_gff_and_gbk', |
| 93 : | jared | 1.3 | start_locally => 1, |
| 94 : | jared | 1.1 | )], |
| 95 : | ]; | ||
| 96 : | } | ||
| 97 : | |||
| 98 : | arodri7 | 1.8 | sub figfam_process { |
| 99 : | return [[uploaded => \&process_upload], | ||
| 100 : | [preprocess => ClusterStage->new('mg_preprocess', | ||
| 101 : | sge_flag => "-l mg_preprocess", | ||
| 102 : | )], | ||
| 103 : | [dereplication => ClusterStage->new('mg_check_sequence_distribution', | ||
| 104 : | start_locally => 1, | ||
| 105 : | )], | ||
| 106 : | arodri7 | 1.11 | [figfam_server => ClusterStage->new('mg_ff_server', |
| 107 : | arodri7 | 1.8 | sge_flag => "-l mg_ff_server", |
| 108 : | )], | ||
| 109 : | [figfam_sims => ClusterStage->new('mg_figfam_sims', | ||
| 110 : | start_locally => 1, | ||
| 111 : | )], | ||
| 112 : | [non_figfam_sims => ClusterStage->new('mg_non_figfam_sims', | ||
| 113 : | start_locally => 1, | ||
| 114 : | )], | ||
| 115 : | arodri7 | 1.12 | [non_seed_sims => ClusterStage->new('mg_non_seed_sims', |
| 116 : | arodri7 | 1.8 | start_locally => 1, |
| 117 : | )], | ||
| 118 : | arodri7 | 1.12 | [check_all_sims => ClusterStage->new('mg_check_all_sims', |
| 119 : | arodri7 | 1.8 | start_locally => 1, |
| 120 : | )], | ||
| 121 : | [create_seed_org => ClusterStage->new('mg_create_seed_org', | ||
| 122 : | sge_flag => "-l mg_postproc_taxa_sims", | ||
| 123 : | )], | ||
| 124 : | [export_to_genbank => ClusterStage->new('mg_sims_to_gff_and_gbk', | ||
| 125 : | start_locally => 1, | ||
| 126 : | )], | ||
| 127 : | ]; | ||
| 128 : | } | ||
| 129 : | |||
| 130 : | |||
| 131 : | jared | 1.1 | ######################################## |
| 132 : | # | ||
| 133 : | # Pipeline Stages | ||
| 134 : | # | ||
| 135 : | ######################################### | ||
| 136 : | |||
| 137 : | sub process_upload | ||
| 138 : | { | ||
| 139 : | return; | ||
| 140 : | } | ||
| 141 : | |||
| 142 : | sub mark_job_done | ||
| 143 : | { | ||
| 144 : | |||
| 145 : | print "Attempting to Email user\n"; | ||
| 146 : | jared | 1.2 | |
| 147 : | jared | 1.1 | my($job_id, $job_dir, $meta, $req) = @_; |
| 148 : | |||
| 149 : | if (open(D, ">$job_dir/DONE")) | ||
| 150 : | { | ||
| 151 : | print D time . "\n"; | ||
| 152 : | close(D); | ||
| 153 : | } | ||
| 154 : | else | ||
| 155 : | { | ||
| 156 : | warn "Error opening $job_dir/DONE: $!\n"; | ||
| 157 : | } | ||
| 158 : | |||
| 159 : | my $job = new Job48($job_id); | ||
| 160 : | |||
| 161 : | my $userobj = $job->getUserObject(); | ||
| 162 : | |||
| 163 : | print "setting meta $meta\n"; | ||
| 164 : | $meta->set_metadata("status.final","complete"); | ||
| 165 : | print "setting meta $meta .. done\n"; | ||
| 166 : | |||
| 167 : | if ($userobj) | ||
| 168 : | { | ||
| 169 : | my $email = $userobj->email(); | ||
| 170 : | my $name = join(" " , $userobj->firstname(), $userobj->lastname()); | ||
| 171 : | |||
| 172 : | my $full = $name ? "$name <$email>" : $email; | ||
| 173 : | print "send email to $full\n"; | ||
| 174 : | |||
| 175 : | my $mail = Mail::Mailer->new(); | ||
| 176 : | $mail->open({ | ||
| 177 : | To => $full, | ||
| 178 : | From => 'Metagenome RAST server <mg-rast@mcs.anl.gov>', | ||
| 179 : | Subject => "MG-RAST job completed" | ||
| 180 : | }); | ||
| 181 : | |||
| 182 : | my $gname = $job->genome_name; | ||
| 183 : | my $entry = $FIG_Config::fortyeight_home; | ||
| 184 : | $entry = "http://metagenomics.nmpdr.org/" if $entry eq ''; | ||
| 185 : | print $mail "The annotation job that you submitted for $gname has completed.\n"; | ||
| 186 : | print $mail "It is available for browsing at $entry as job number $job_id.\n"; | ||
| 187 : | $mail->close(); | ||
| 188 : | } | ||
| 189 : | } |
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