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| 1 : | parrello | 1.1 | #!/usr/bin/perl -w |
| 2 : | |||
| 3 : | # | ||
| 4 : | # Copyright (c) 2003-2006 University of Chicago and Fellowship | ||
| 5 : | # for Interpretations of Genomes. All Rights Reserved. | ||
| 6 : | # | ||
| 7 : | # This file is part of the SEED Toolkit. | ||
| 8 : | # | ||
| 9 : | # The SEED Toolkit is free software. You can redistribute | ||
| 10 : | # it and/or modify it under the terms of the SEED Toolkit | ||
| 11 : | # Public License. | ||
| 12 : | # | ||
| 13 : | # You should have received a copy of the SEED Toolkit Public License | ||
| 14 : | # along with this program; if not write to the University of Chicago | ||
| 15 : | # at info@ci.uchicago.edu or the Fellowship for Interpretation of | ||
| 16 : | # Genomes at veronika@thefig.info or download a copy from | ||
| 17 : | # http://www.theseed.org/LICENSE.TXT. | ||
| 18 : | # | ||
| 19 : | |||
| 20 : | package AnnotationSproutLoader; | ||
| 21 : | |||
| 22 : | use strict; | ||
| 23 : | use Tracer; | ||
| 24 : | use ERDB; | ||
| 25 : | use base 'BaseSproutLoader'; | ||
| 26 : | |||
| 27 : | =head1 Sprout Annotation Load Group Class | ||
| 28 : | |||
| 29 : | =head2 Introduction | ||
| 30 : | |||
| 31 : | The Load Group includes all of the major annotation data tables. | ||
| 32 : | |||
| 33 : | =head3 new | ||
| 34 : | |||
| 35 : | my $sl = SproutLoader->new($erdb, $source, $options, @tables); | ||
| 36 : | |||
| 37 : | Construct a new SproutLoader object. | ||
| 38 : | |||
| 39 : | =over 4 | ||
| 40 : | |||
| 41 : | =item erdb | ||
| 42 : | |||
| 43 : | [[SproutPm]] object for the database being loaded. | ||
| 44 : | |||
| 45 : | =item options | ||
| 46 : | |||
| 47 : | Reference to a hash of command-line options. | ||
| 48 : | |||
| 49 : | =item tables | ||
| 50 : | |||
| 51 : | List of tables in this load group. | ||
| 52 : | |||
| 53 : | =back | ||
| 54 : | |||
| 55 : | =cut | ||
| 56 : | |||
| 57 : | sub new { | ||
| 58 : | # Get the parameters. | ||
| 59 : | parrello | 1.2 | my ($class, $erdb, $options) = @_; |
| 60 : | parrello | 1.1 | # Create the table list. |
| 61 : | my @tables = sort qw(Annotation IsTargetOfAnnotation SproutUser MadeAnnotation); | ||
| 62 : | # Create the BaseSproutLoader object. | ||
| 63 : | parrello | 1.2 | my $retVal = BaseSproutLoader::new($class, $erdb, $options, @tables); |
| 64 : | parrello | 1.1 | # Return it. |
| 65 : | return $retVal; | ||
| 66 : | } | ||
| 67 : | |||
| 68 : | =head2 Public Methods | ||
| 69 : | |||
| 70 : | =head3 Generate | ||
| 71 : | |||
| 72 : | $sl->Generate(); | ||
| 73 : | |||
| 74 : | Generate the data for the annotation data files. | ||
| 75 : | |||
| 76 : | =cut | ||
| 77 : | |||
| 78 : | sub Generate { | ||
| 79 : | # Get the parameters. | ||
| 80 : | my ($self) = @_; | ||
| 81 : | # Get the sprout object. | ||
| 82 : | my $sprout = $self->db(); | ||
| 83 : | # Get the FIG object. | ||
| 84 : | my $fig = $self->source(); | ||
| 85 : | # Check for global mode. | ||
| 86 : | if ($self->global()) { | ||
| 87 : | # In global mode, we create the built-in users. | ||
| 88 : | Trace("Creating default users.") if T(3); | ||
| 89 : | $self->PutE(SproutUser => "FIG", description => "Fellowship for Interpretation of Genomes"); | ||
| 90 : | $self->PutE(SproutUser => "FIG", description => "Fellowship for Interpretation of Genomes"); | ||
| 91 : | } else { | ||
| 92 : | # Get the section ID, which is the relevant genome. | ||
| 93 : | my $genomeID = $self->section(); | ||
| 94 : | # Process the annotations for the specified genome. | ||
| 95 : | # Get the current time. | ||
| 96 : | my $time = time(); | ||
| 97 : | # Create a hash of timestamps. We use this to prevent duplicate time stamps | ||
| 98 : | # from showing up for a single PEG's annotations. | ||
| 99 : | my %seenTimestamps = (); | ||
| 100 : | # Get the genome's annotations. | ||
| 101 : | my @annotations = $fig->read_all_annotations($genomeID); | ||
| 102 : | Trace("Processing annotations.") if T(2); | ||
| 103 : | for my $tuple (@annotations) { | ||
| 104 : | # Get the annotation tuple. | ||
| 105 : | my ($peg, $timestamp, $user, $text) = @{$tuple}; | ||
| 106 : | # Change assignments by the master user to FIG assignments. | ||
| 107 : | $text =~ s/Set master function/Set FIG function/s; | ||
| 108 : | # Insure the time stamp is valid. | ||
| 109 : | if ($timestamp =~ /^\d+$/) { | ||
| 110 : | # Here it's a number. We need to insure the one we use to form | ||
| 111 : | # the key is unique. | ||
| 112 : | my $keyStamp = $timestamp; | ||
| 113 : | while ($seenTimestamps{"$peg:$keyStamp"}) { | ||
| 114 : | $keyStamp++; | ||
| 115 : | } | ||
| 116 : | my $annotationID = "$peg:$keyStamp"; | ||
| 117 : | $seenTimestamps{$annotationID} = 1; | ||
| 118 : | # Insure the user exists. | ||
| 119 : | parrello | 1.2 | $self->PutE(SproutUser => $user, description => "SEED user"); |
| 120 : | parrello | 1.1 | # Generate the annotation. |
| 121 : | parrello | 1.2 | $self->PutE(Annotation => $annotationID, time => $timestamp, |
| 122 : | parrello | 1.1 | annotation => $text); |
| 123 : | $self->PutR(IsTargetOfAnnotation => $peg, $annotationID); | ||
| 124 : | $self->PutR(MadeAnnotation => $user, $annotationID); | ||
| 125 : | } else { | ||
| 126 : | # Here we have an invalid time stamp. | ||
| 127 : | Trace("Invalid time stamp \"$timestamp\" in annotations for $peg.") if T(1); | ||
| 128 : | } | ||
| 129 : | } | ||
| 130 : | } | ||
| 131 : | } | ||
| 132 : | |||
| 133 : | |||
| 134 : | 1; |
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