-
Notifications
You must be signed in to change notification settings - Fork 28
/
project.pm
296 lines (264 loc) · 12.4 KB
/
project.pm
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
package resources::project;
use strict;
use warnings;
no warnings('once');
use Conf;
use parent qw(resources::resource);
# Override parent constructor
sub new {
my ($class, @args) = @_;
# Call the constructor of the parent class
my $self = $class->SUPER::new(@args);
# Add name / attributes
my %rights = $self->user ? map {$_, 1} @{$self->user->has_right_to(undef, 'view', 'project')} : ();
$self->{name} = "project";
$self->{rights} = \%rights;
$self->{attributes} = { "id" => [ 'string', 'unique object identifier' ],
"name" => [ 'string', 'human readable identifier' ],
"libraries" => [ 'list', [ 'reference library', 'a list of references to the related library objects' ] ],
"samples" => [ 'list', [ 'reference sample', 'a list of references to the related sample objects' ] ],
"metagenomes" => [ 'list', [ 'reference metagenome', 'a list of references to the related metagenome objects' ] ],
"description" => [ 'string', 'a short, comprehensive description of the project' ],
"funding_source" => [ 'string', 'the official name of the source of funding of this project' ],
"pi" => [ 'string', 'the first and last name of the principal investigator of the project' ],
"metadata" => [ 'hash', 'key value pairs describing metadata' ],
"created" => [ 'date', 'time the object was first created' ],
"version" => [ 'integer', 'version of the object' ],
"url" => [ 'uri', 'resource location of this object instance' ],
"status" => [ 'cv', [ ['public', 'object is public'],
['private', 'object is private'] ] ]
};
return $self;
}
# resource is called without any parameters
# this method must return a description of the resource
sub info {
my ($self) = @_;
my $content = { 'name' => $self->name,
'url' => $self->cgi->url."/".$self->name,
'description' => "A project is a composition of samples, libraries and metagenomes being analyzed in a global context.",
'type' => 'object',
'documentation' => $self->cgi->url.'/api.html#'.$self->name,
'requests' => [ { 'name' => "info",
'request' => $self->cgi->url."/".$self->name,
'description' => "Returns description of parameters and attributes.",
'method' => "GET" ,
'type' => "synchronous" ,
'attributes' => "self",
'parameters' => { 'options' => {},
'required' => {},
'body' => {} } },
{ 'name' => "query",
'request' => $self->cgi->url."/".$self->name,
'description' => "Returns a set of data matching the query criteria.",
'example' => [ $self->cgi->url."/".$self->name."?limit=20&order=name",
'retrieve the first 20 projects ordered by name' ],
'method' => "GET" ,
'type' => "synchronous" ,
'attributes' => { "next" => [ "uri", "link to the previous set or null if this is the first set" ],
"prev" => [ "uri", "link to the next set or null if this is the last set" ],
"order" => [ "string", "name of the attribute the returned data is ordered by" ],
"data" => [ "list", [ "object", [$self->attributes, "list of the project objects"] ] ],
"limit" => [ "integer", "maximum number of data items returned, default is 10" ],
"total_count" => [ "integer", "total number of available data items" ],
"offset" => [ "integer", "zero based index of the first returned data item" ] },
'parameters' => { 'options' => { 'verbosity' => [ 'cv', [ [ 'minimal', 'returns only minimal information' ],
[ 'verbose', 'returns all metadata' ],
[ 'full', 'returns all metadata and references' ] ] ],
'limit' => [ 'integer', 'maximum number of items requested' ],
'offset' => [ 'integer', 'zero based index of the first data object to be returned' ],
'order' => [ 'cv', [ [ 'id' , 'return data objects ordered by id' ],
[ 'name' , 'return data objects ordered by name' ] ] ] },
'required' => {},
'body' => {} } },
{ 'name' => "instance",
'request' => $self->cgi->url."/".$self->name."/{ID}",
'description' => "Returns a single data object.",
'example' => [ $self->cgi->url."/".$self->name."/mgp128?verbosity=full",
'retrieve all data for project mgp128' ],
'method' => "GET" ,
'type' => "synchronous" ,
'attributes' => $self->attributes,
'parameters' => { 'options' => { 'verbosity' => [ 'cv', [ [ 'minimal', 'returns only minimal information' ],
[ 'verbose', 'returns all metadata' ],
[ 'full', 'returns all metadata and references' ] ] ] },
'required' => { "id" => [ "string", "unique object identifier" ] },
'body' => {} } },
]
};
$self->return_data($content);
}
# the resource is called with an id parameter
sub instance {
my ($self) = @_;
# check id format
my $rest = $self->rest;
my ($id) = $rest->[0] =~ /^mgp(\d+)$/;
if ((! $id) && scalar(@$rest)) {
$self->return_data( {"ERROR" => "invalid id format: " . $rest->[0]}, 400 );
}
# get database
my $master = $self->connect_to_datasource();
# check if this is an action request
my $requests = { 'movemetagenomes' => 1 };
if (scalar(@$rest) > 1 && $requests->{$rest->[1]}) {
# move metagenomes to a different project
if ($rest->[1] eq 'movemetagenomes') {
unless ($self->user->has_star_right('edit', 'user')) {
$self->return_data( {"ERROR" => "insufficient permissions for this user call"}, 401 );
}
my ($id2) = $self->cgi->param('target') =~ /^mgp(\d+)$/;
if (! $id2) {
$self->return_data( {"ERROR" => "invalid id format: " . $self->cgi->param('target')}, 400 );
}
my $project_a = $master->Project->init( {id => $id} );
my $project_b = $master->Project->init( {id => $id2} );
unless (ref($project_a) && ref($project_b)) {
$self->return_data( {"ERROR" => "id $id or $id2 does not exists"}, 404 );
}
my $proj_job = $master->ProjectJob->get_objects({ project => $project_a });
my $job_a_hash = {};
foreach my $j (@$proj_job) {
$job_a_hash->{$j->job->{metagenome_id}} = $j->job;
}
my @move_over = $self->cgi->param("move");
foreach my $m (@move_over) {
$m =~ s/^mgm//;
unless ($job_a_hash->{$m}) {
$self->return_data( {"ERROR" => "metagenome not part of source project: " . $m}, 400 );
}
}
foreach my $m (@move_over) {
my $job = $master->Job->get_objects( { metagenome_id => $m });
if (scalar(@$job)) {
$job = $job->[0];
$project_a->remove_job($job);
$project_b->add_job($job);
}
}
$self->return_data( {"OK" => "metagenomes moved"}, 200 );
}
}
# get data
my $project = $master->Project->init( {id => $id} );
unless (ref($project)) {
$self->return_data( {"ERROR" => "id $id does not exists"}, 404 );
}
# check rights
unless ($project->{public} || exists($self->rights->{$id}) || exists($self->rights->{'*'})) {
$self->return_data( {"ERROR" => "insufficient permissions to view this data"}, 401 );
}
# return cached if exists
$self->return_cached();
# prepare data
my $data = $self->prepare_data( [$project] );
$data = $data->[0];
$self->return_data($data, undef, 1); # cache this!
}
# the resource is called without an id parameter, but with at least one query parameter
sub query {
my ($self) = @_;
# get database
my $master = $self->connect_to_datasource();
my $projects = [];
my $total = 0;
# check pagination
my $limit = defined($self->cgi->param('limit')) ? $self->cgi->param('limit') : 10;
my $offset = $self->cgi->param('offset') || 0;
my $order = $self->cgi->param('order') || "id";
if ($limit == 0) {
$limit = 18446744073709551615;
}
# check if we just want the private projects
if ($self->cgi->param('private')) {
unless ($self->user) {
$self->return_data({"ERROR" => "private option requires authentication"}, 400);
}
my $ids = [];
if ($self->cgi->param('edit')) {
$ids = $self->user->has_right_to(undef, 'edit', 'project');
} else {
$ids = $self->user->has_right_to(undef, 'view', 'project');
}
if (scalar(@$ids) && $ids->[0] eq '*') {
shift @$ids;
}
my $list = join(",", @$ids);
$total = scalar(@$ids);
$projects = $master->Project->get_objects( {$order => [undef, "id IN ($list) ORDER BY $order LIMIT $limit OFFSET $offset"]} );
}
# get all items the user has access to
elsif (exists $self->rights->{'*'}) {
$total = $master->Project->count_all();
$projects = $master->Project->get_objects( {$order => [undef, "_id IS NOT NULL ORDER BY $order LIMIT $limit OFFSET $offset"]} );
} else {
my $public = $master->Project->get_public_projects(1);
my $list = join(',', (@$public, keys %{$self->rights}));
$total = scalar(@$public) + scalar(keys %{$self->rights});
$projects = $master->Project->get_objects( {$order => [undef, "id IN ($list) ORDER BY $order LIMIT $limit OFFSET $offset"]} );
}
$limit = ($limit > scalar(@$projects)) ? scalar(@$projects) : $limit;
# prepare data to the correct output format
my $data = $self->prepare_data($projects);
# check for pagination
$data = $self->check_pagination($data, $total, $limit);
$self->return_data($data);
}
# reformat the data into the requested output format
sub prepare_data {
my ($self, $data) = @_;
my $objects = [];
foreach my $project (@$data) {
my $url = $self->cgi->url;
my $obj = {};
$obj->{id} = "mgp".$project->id;
$obj->{name} = $project->name;
$obj->{pi} = $project->pi;
$obj->{status} = $project->public ? 'public' : 'private';
$obj->{version} = 1;
$obj->{url} = $url.'/project/'.$obj->{id};
$obj->{created} = "";
if ($self->cgi->param('verbosity')) {
if ($self->cgi->param('verbosity') eq 'full') {
my @jobs = map { ["mgm".$_, $url.'/metagenome/mgm'.$_] } @{ $project->all_metagenome_ids };
my @colls = @{ $project->collections };
my @samples = map { ["mgs".$_->{ID}, $url."/sample/mgs".$_->{ID}] } grep { $_ && ref($_) && ($_->{type} eq 'sample') } @colls;
my @libraries = map { ["mgl".$_->{ID}, $url."/library/mgl".$_->{ID}] } grep { $_ && ref($_) && ($_->{type} eq 'library') } @colls;
$obj->{metagenomes} = \@jobs;
$obj->{samples} = \@samples;
$obj->{libraries} = \@libraries;
}
if (($self->cgi->param('verbosity') eq 'verbose') || ($self->cgi->param('verbosity') eq 'full') || ($self->cgi->param('verbosity') eq 'summary')) {
my $metadata = $project->data();
my $desc = $metadata->{project_description} || $metadata->{study_abstract} || " - ";
my $fund = $metadata->{project_funding} || " - ";
$obj->{metadata} = $metadata;
$obj->{description} = $desc;
$obj->{funding_source} = $fund;
if ($self->cgi->param('verbosity') eq 'summary') {
my $jdata = $project->metagenomes_summary();
$obj->{metagenomes} = [];
foreach my $row (@$jdata) {
push(@{$obj->{metagenomes}}, { metagenome_id => $row->[0],
name => $row->[1],
basepairs => $row->[2],
sequences => $row->[3],
biome => $row->[4],
feature => $row->[5],
material => $row->[6],
location => $row->[7],
country => $row->[8],
coordinates => $row->[9],
sequence_type => $row->[10],
sequencing_method => $row->[11] });
}
}
} elsif ($self->cgi->param('verbosity') ne 'minimal') {
$self->return_data( {"ERROR" => "invalid value for option verbosity"}, 400 );
}
}
push @$objects, $obj;
}
return $objects;
}
1;