File Coverage

blib/lib/HackaMol/Roles/FileFetchRole.pm
Criterion Covered Total %
statement 18 44 40.9
branch 0 8 0.0
condition 0 3 0.0
subroutine 6 9 66.6
pod 2 2 100.0
total 26 66 39.3


line stmt bran cond sub pod time code
1             $HackaMol::Roles::FileFetchRole::VERSION = '0.052';
2             #ABSTRACT: Role for using LWP::Simple to fetch files from www
3             use Moose::Role;
4 11     11   5143 use Carp;
  11         31  
  11         70  
5 11     11   47911 use Path::Tiny;
  11         30  
  11         582  
6 11     11   75 use HTTP::Tiny;
  11         25  
  11         474  
7 11     11   7733 #use LWP::Simple;
  11         340869  
  11         443  
8             use Data::Dumper;
9 11     11   7021  
  11         57927  
  11         3206  
10             has 'pdbserver', is => 'rw', isa => 'Str', lazy => 1, default => 'https://files.rcsb.org/download/';
11             has 'overwrite', is => 'rw', isa => 'Bool', lazy => 1, default => 0;
12              
13             my $pdbid = shift;
14             $pdbid =~ s/\.pdb//; #just in case
15 0     0     $pdbid .= '.pdb';
16 0           return $pdbid;
17 0           }
18 0            
19             #return pdb contents downloaded from pdb.org
20             my $self = shift;
21             my $pdbid = _fix_pdbid(shift);
22             my ($ok, $why) = HTTP::Tiny->can_ssl;
23 0     0 1   if ($ok){
24 0           my $pdb = HTTP::Tiny->new->get($self->pdbserver.$pdbid);
25 0           return ( $pdb->{content} );
26 0 0         }
27 0           else {
28 0           warn "$why";
29             return 0;
30             }
31 0           }
32 0            
33             #return array of lines from pdb downloaded from pdb.org
34             my $self = shift;
35             my $pdbid = _fix_pdbid(shift);
36             my $fpdbid = shift ;
37             $fpdbid = $pdbid unless defined($fpdbid);
38 0     0 1   $fpdbid = path($fpdbid);
39 0            
40 0           if ($fpdbid->exists and not $self->overwrite){
41 0 0         carp "$fpdbid exists, set self->overwrite(1) to overwrite";
42 0           return $fpdbid->stringify;
43             }
44 0 0 0       my $pdb = $self->get_pdbid( $pdbid );
45 0          
46 0           if ($pdb){
47             $fpdbid->spew($pdb);
48 0           return ( $fpdbid->stringify );
49             }
50 0 0         else{
51 0           warn "could not connect, $fpdbid not written\n";
52 0           return 0;
53             }
54             }
55 0            
56 0           no Moose::Role;
57             1;
58              
59              
60 11     11   87 =pod
  11         25  
  11         119  
61              
62             =head1 NAME
63              
64             HackaMol::Roles::FileFetchRole - Role for using LWP::Simple to fetch files from www
65              
66             =head1 VERSION
67              
68             version 0.052
69              
70             =head1 SYNOPSIS
71              
72             use HackaMol;
73              
74             my $pdb = $HackaMol->new->get_pdbid("2cba");
75             print $pdb;
76              
77             =head1 DESCRIPTION
78              
79             FileFetchRole provides attributes and methods for pulling files from the internet.
80             Currently, the Role has one method and one attribute for interacting with the Protein Database.
81              
82             =head1 METHODS
83              
84             =head2 get_pdbid
85              
86             fetches a pdb from pdb.org and returns the file in a string.
87              
88             =head2 getstore_pdbid
89              
90             arguments: pdbid and filename for writing (optional).
91             Fetches a pdb from pdb.org and stores it in your working directory unless {it exists and overwrite(0)}. If a filename is not
92             passed to the method, it will write to $pdbid.pdb. use get_pdbid to return contents
93              
94             =head1 ATTRIBUTES
95              
96             =head2 overwrite
97              
98             isa lazy ro Bool that defaults to 0 (false). If overwrite(1), then fetched files will be able to overwrite
99             those of same name in working directory.
100              
101             =head2 pdbserver
102              
103             isa lazy rw Str that defaults to http://pdb.org/pdb/files/
104              
105             =head1 SEE ALSO
106              
107             =over 4
108              
109             =item *
110              
111             L<http://www.pdb.org>
112              
113             =item *
114              
115             L<LWP::Simple>
116              
117             =back
118              
119             =head1 AUTHOR
120              
121             Demian Riccardi <demianriccardi@gmail.com>
122              
123             =head1 COPYRIGHT AND LICENSE
124              
125             This software is copyright (c) 2017 by Demian Riccardi.
126              
127             This is free software; you can redistribute it and/or modify it under
128             the same terms as the Perl 5 programming language system itself.
129              
130             =cut