forked from tripal/tripal_blast
-
Notifications
You must be signed in to change notification settings - Fork 2
/
blast_ui.module
275 lines (234 loc) · 7.54 KB
/
blast_ui.module
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
<?php
/**
* @file
* The main file for the blast UI module.
*/
// BLAST Submission Forms
require_once 'includes/blast_ui.form_common.inc';
require_once 'includes/blast_ui.form_advanced_options.inc';
// NOTE: The forms themeselves are included using hook_menu to ensure they
// are only included when needed.
// BLAST DB Node functionality
require_once 'includes/blast_ui.node.inc';
// BLAST Link-out functionality.
require_once 'includes/blast_ui.linkouts.inc';
// Functions specific to themeing (ie: preprocess)
require_once 'theme/blast_ui.theme.inc';
// Application Programmers Interface
require_once 'api/blast_ui.api.inc';
// Administration
require_once 'includes/blast_ui.admin.inc';
/**
* Implements hook_menu().
*/
function blast_ui_menu() {
// BLAST DB Node
$items['node__blastdb'] = array(
'template' => 'node--blastdb',
'render element' => 'node',
'base hook' => 'node',
'path' => 'theme',
);
// Single All-in-One BLAST submission form
$items['blast'] = array(
'title' => 'BLAST',
'page callback' => 'drupal_get_form',
'page arguments' => array('blast_ui_all_in_one_form'),
'access arguments' => array('access content'),
'file' => 'includes/blast_ui.form_single.inc',
'type' => MENU_NORMAL_ITEM,
'expanded' => TRUE,
);
// Per Query Type BLAST submission forms
$items['blast/nucleotide'] = array(
'title' => 'Nucleotide Query',
'page callback' => 'drupal_get_form',
'page arguments' => array('blast_ui_per_query_type_form', 1, 2),
'access arguments' => array('access content'),
'file' => 'includes/blast_ui.form_per_query_type.inc',
'type' => MENU_NORMAL_ITEM,
'expanded' => TRUE,
);
$items['blast/protein'] = array(
'title' => 'Protein Query',
'page callback' => 'drupal_get_form',
'page arguments' => array('blast_ui_per_query_type_form', 1),
'access arguments' => array('access content'),
'file' => 'includes/blast_ui.form_per_query_type.inc',
'type' => MENU_NORMAL_ITEM,
'expanded' => TRUE,
);
// Per BLAST-program submission forms
$items['blast/nucleotide/nucleotide'] = array(
'title' => 'BLASTn',
'page callback' => 'drupal_get_form',
'page arguments' => array('blast_ui_per_blast_program_form', 1, 2),
'access arguments' => array('access content'),
'file' => 'includes/blast_ui.form_per_program.inc',
'type' => MENU_NORMAL_ITEM
);
$items['blast/nucleotide/protein'] = array(
'title' => 'BLASTx',
'page callback' => 'drupal_get_form',
'page arguments' => array('blast_ui_per_blast_program_form', 1, 2),
'access arguments' => array('access content'),
'file' => 'includes/blast_ui.form_per_program.inc',
'type' => MENU_NORMAL_ITEM
);
$items['blast/protein/nucleotide'] = array(
'title' => 'tBLASTn',
'page callback' => 'drupal_get_form',
'page arguments' => array('blast_ui_per_blast_program_form', 1, 2),
'access arguments' => array('access content'),
'file' => 'includes/blast_ui.form_per_program.inc',
'type' => MENU_NORMAL_ITEM
);
$items['blast/protein/protein'] = array(
'title' => 'BLASTp',
'page callback' => 'drupal_get_form',
'page arguments' => array('blast_ui_per_blast_program_form', 1, 2),
'access arguments' => array('access content'),
'file' => 'includes/blast_ui.form_per_program.inc',
'type' => MENU_NORMAL_ITEM
);
// BLAST Results page
$items['blast/report/%'] = array(
'title' => 'BLAST Results',
'page callback' => 'show_blast_output',
'page arguments' => array(2),
'access arguments' => array('access content'),
'type' => MENU_CALLBACK,
);
// BLAST Admin
$items['admin/tripal/extension/tripal_blast'] = array(
'title' => 'Tripal BLAST User Interface',
'description' => 'Provides an interface allowing users to execute their own BLASTs.',
'page callback' => 'drupal_get_form',
'page arguments' => array('blast_ui_admin_form'),
'access arguments' => array('administer tripal'),
'type' => MENU_NORMAL_ITEM,
);
$items['admin/tripal/extension/tripal_blast/blast_ui'] = array(
'title' => 'BLAST UI',
'type' => MENU_DEFAULT_LOCAL_TASK,
);
$items['admin/tripal/extension/tripal_blast/help'] = array(
'title' => 'Help',
'page callback' => 'theme',
'page arguments' => array('blast_help'),
'access arguments' => array('administer tripal'),
'type' => MENU_LOCAL_TASK,
);
return $items;
}
/**
* Implements hook_theme().
*/
function blast_ui_theme() {
$items = array();
$path = drupal_get_path('module', 'blast_ui');
// Displays the BLAST results for each job
$items['show_blast_report'] = array(
'template' => 'blast_report',
'path' => "$path/theme",
);
// Displays the BLAST results for each job
$items['blast_report_pending'] = array(
'template' => 'blast_report_pending',
'path' => "$path/theme",
);
// Themes the alignments in a BLAST result display
$items['blast_report_alignment_row'] = array(
'template' => 'blast_report_alignment_row',
'variables' => array('hsps' => NULL),
'path' => "$path/theme",
);
// Lists the recent blast jobs for a given user/session.
$items['blast_recent_jobs'] = array(
'template' => 'blast_recent_jobs',
'variables' => array('programs' => NULL),
'path' => "$path/theme",
);
// Module Help
$items['blast_help'] = array(
'template' => 'blast_help',
'path' => "$path/theme",
);
// Menu Information Pages
// These are only seen if the user has disabled the all-in-one
// or by query type forms.
$items['blast_user_menupage'] = array(
'template' => 'blast_user_menupage',
'path' => "$path/theme",
);
$items['blast_nucleotide_user_menupage'] = array(
'template' => 'blast_nucleotide_user_menupage',
'path' => "$path/theme",
);
$items['blast_protein_user_menupage'] = array(
'template' => 'blast_protein_user_menupage',
'path' => "$path/theme",
);
return $items;
}
/**
* Implements hook_help().
*/
function blast_ui_help($path, $arg) {
if ($path == 'admin/help#blast_ui') {
return theme('blast_help');
}
}
/**
* Facilitate presenting the result of the blast search
*
* @param $job_id
* The tripal job_id of the BLAST job previously submitted
*
* @return $result
* Return HTML output of the BLAST results to be displayed to the user
*
*/
function show_blast_output($job_string) {
// BLASTs are run as a Tripal job. As such we need to determine whether the current
// BLAST is in the queue, running or complete in order to determine what to show the user
//decode the job_id
$job_id = blast_ui_reveal_secret($job_string);
$job = tripal_get_job($job_id);
// 1) Job is in the Queue
if ($job->start_time === NULL AND $job->end_time == NULL) {
return theme('blast_report_pending', array('status_code' => 0, 'status' => 'Pending'));
}
// 2) Job has been Cancelled
elseif ($job->status == 'Cancelled') {
return theme('blast_report_pending', array('status_code' => 999, 'status' => 'Cancelled'));
}
// 3) Job is Complete
elseif ($job->end_time !== NULL) {
// Return the Results :)
return theme('show_blast_report', array('job_id' => $job_id));
}
// 4) Job is in Progress
else {
return theme('blast_report_pending', array('status_code' => 1, 'status' => 'Running'));
}
return '';
}
/**
* Enable web services API
*
* @param $owner
*
* @param $api
*
* @return $result
*
*/
function blast_ui_ctools_plugin_api($owner, $api) {
if ($owner == 'services' && $api == 'services') {
return array(
'version' => 3,
'file' => 'includes/blast_ui.services.inc'
);
}
}