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1 package Bio::EnsEMBL::Pipeline::FASTA::EmailSummary;
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2
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3 use strict;
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4 use warnings;
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5 use base qw/Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail Bio::EnsEMBL::Pipeline::Base/;
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6 use Bio::EnsEMBL::Hive::Utils qw/destringify/;
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7
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8 sub fetch_input {
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9 my ($self) = @_;
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10
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11 $self->assert_executable('sendmail');
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12
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13 my $dump_dna = $self->jobs('DumpDNA');
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14 my $copy_dna = $self->jobs('CopyDNA');
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15 my $dump_genes = $self->jobs('DumpGenes');
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16 my $blast_dna = $self->jobs('BlastDNAIndex');
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17 my $blast_gene = $self->jobs('BlastGeneIndex');
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18 my $blast_pep = $self->jobs('BlastPepIndex');
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19 my $blat = $self->jobs('BlatDNAIndex', 100);
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20 my $blat_sm = $self->jobs('BlatSmDNAIndex', 100);
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21
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22 my @args = (
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23 $dump_dna->{successful_jobs},
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24 $dump_dna->{failed_jobs},
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25 $copy_dna->{successful_jobs},
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26 $copy_dna->{failed_jobs},
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27 $dump_genes->{successful_jobs},
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28 $dump_genes->{failed_jobs},
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29 $blast_dna->{successful_jobs},
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30 $blast_dna->{failed_jobs},
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31 $blast_gene->{successful_jobs},
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32 $blast_gene->{failed_jobs},
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33 $blast_pep->{successful_jobs},
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34 $blast_pep->{failed_jobs},
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35 $blat->{successful_jobs},
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36 $blat->{failed_jobs},
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37 $blat_sm->{successful_jobs},
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38 $blat_sm->{failed_jobs},
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39 $self->failed(),
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40 $self->summary($dump_dna),
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41 $self->summary($copy_dna),
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42 $self->summary($dump_genes),
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43 $self->summary($blast_dna),
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44 $self->summary($blast_gene),
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45 $self->summary($blast_pep),
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46 $self->summary($blat),
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47 $self->summary($blat_sm),
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48 );
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49
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50 my $msg = sprintf(<<'MSG', @args);
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51 Your FASTA Pipeline has finished. We have:
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52
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53 * %d species with new DNA Dumped (%d failed)
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54 * %d species with copied DNA (%d failed)
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55 * %d species with genes dumped (%d failed)
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56 * %d species with BLAST DNA indexes generated (%d failed)
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57 * %d species with BLAST GENE indexes generated (%d failed)
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58 * %d species with BLAST PEPTIDE indexes generated (%d failed)
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59 * %d species with BLAT DNA generated (%d failed)
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60 * %d species with BLAT soft-masked DNA generated (%d failed)
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61
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62 %s
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63
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64 ===============================================================================
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65
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66 Full breakdown follows ...
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67
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68 %s
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69
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70 %s
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71
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72 %s
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73
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74 %s
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75
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76 %s
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77
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78 %s
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79
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80 %s
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81
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82 %s
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83
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84 MSG
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85 $self->param('text', $msg);
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86 return;
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87 }
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88
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89 sub jobs {
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90 my ($self, $logic_name, $minimum_runtime) = @_;
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91 my $aa = $self->db->get_AnalysisAdaptor();
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92 my $aja = $self->db->get_AnalysisJobAdaptor();
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93 my $analysis = $aa->fetch_by_logic_name($logic_name);
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94 my $id = $analysis->dbID();
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95 my @jobs = @{$aja->generic_fetch("j.analysis_id =$id")};
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96 $_->{input} = destringify($_->input_id()) for @jobs;
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97 @jobs =
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98 sort { $a->{input}->{species} cmp $b->{input}->{species} }
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99 grep {
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100 if($minimum_runtime) {
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101 if($minimum_runtime > $_->runtime_msec()) {
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102 1;
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103 }
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104 else {
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105 0;
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106 }
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107 }
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108 else {
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109 1;
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110 }
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111 }
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112 @jobs;
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113 my %passed_species = map { $_->{input}->{species}, 1 } grep { $_->status() eq 'DONE' } @jobs;
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114 my %failed_species = map { $_->{input}->{species}, 1 } grep { $_->status() eq 'FAILED' } @jobs;
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115 return {
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116 analysis => $analysis,
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117 name => $logic_name,
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118 jobs => \@jobs,
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119 successful_jobs => scalar(keys %passed_species),
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120 failed_jobs => scalar(keys %failed_species),
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121 };
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122 }
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123
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124
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125 sub failed {
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126 my ($self) = @_;
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127 my $failed = $self->db()->get_AnalysisJobAdaptor()->fetch_all_failed_jobs();
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128 if(! @{$failed}) {
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129 return 'No jobs failed. Congratulations!';
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130 }
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131 my $output = <<'MSG';
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132 The following jobs have failed during this run. Please check your hive's error msg table for the following jobs:
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133
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134 MSG
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135 foreach my $job (@{$failed}) {
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136 my $analysis = $self->db()->get_AnalysisAdaptor()->fetch_by_dbID($job->analysis_id());
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137 my $line = sprintf(q{ * job_id=%d %s(%5d) input_id='%s'}, $job->dbID(), $analysis->logic_name(), $analysis->dbID(), $job->input_id());
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138 $output .= $line;
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139 $output .= "\n";
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140 }
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141 return $output;
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142 }
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143
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144 my $sorter = sub {
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145 my $status_to_int = sub {
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146 my ($v) = @_;
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147 return ($v->status() eq 'FAILED') ? 0 : 1;
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148 };
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149 my $status_sort = $status_to_int->($a) <=> $status_to_int->($b);
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150 return $status_sort if $status_sort != 0;
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151 return $a->{input}->{species} cmp $b->{input}->{species};
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152 };
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153
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154 sub summary {
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155 my ($self, $data) = @_;
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156 my $name = $data->{name};
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157 my $underline = '~'x(length($name));
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158 my $output = "$name\n$underline\n\n";
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159 my @jobs = @{$data->{jobs}};
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160 if(@jobs) {
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161 foreach my $job (sort $sorter @{$data->{jobs}}) {
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162 my $species = $job->{input}->{species};
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163 $output .= sprintf(" * %s - job_id=%d %s\n", $species, $job->dbID(), $job->status());
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164 }
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165 }
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166 else {
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167 $output .= "No jobs run for this analysis\n";
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168 }
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169 $output .= "\n";
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170 return $output;
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171 }
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172
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173 1; |
