Tripal v1.0 (6.x-1.0)
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00001 <?php 00002 00031 function tripal_feature_views_data() { 00032 $data = array(); 00033 00034 if (module_exists('tripal_views')) { 00035 $tables = array( 00036 'feature', 00037 ); 00038 00039 foreach ($tables as $tablename) { 00040 $priority = 9; 00041 00042 // check to see if the table is integrated. If it is then integrate it's 00043 // corresponding 'chado_[table]' table. 00044 if (!tripal_views_is_integrated($tablename, $priority)) { 00045 $table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename, TRUE, $priority); 00046 00047 // Add in node relationships if chado is in the same db as drupal 00048 if (tripal_core_chado_schema_exists()) { 00049 $integrations = tripal_views_add_node_relationship_to_chado_table_integration($table_integration_array); 00050 foreach ($integrations as $integration) { 00051 tripal_views_integration_add_entry($integration); 00052 } 00053 } 00054 else { 00055 tripal_views_integration_add_entry($table_integration_array); 00056 } 00057 00058 } 00059 } 00060 00061 $tables = array( 00062 'feature_cvterm', 00063 'feature_cvterm_dbxref', 00064 'feature_cvterm_pub', 00065 'feature_cvtermprop', 00066 'feature_dbxref', 00067 'feature_pub', 00068 'feature_pubprop', 00069 'feature_relationship', 00070 'feature_relationship_pub', 00071 'feature_relationshipprop', 00072 'feature_relationshipprop_pub', 00073 'feature_synonym', 00074 'featureloc', 00075 'featureloc_pub', 00076 'featureprop', 00077 'featureprop_pub', 00078 'featuremap', 00079 'featuremap_pub', 00080 'featurepos', 00081 'featurerange' 00082 ); 00083 foreach ($tables as $tablename) { 00084 $priority = 9; 00085 if (!tripal_views_is_integrated($tablename, $priority)) { 00086 $table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename, FALSE, $priority); 00087 tripal_views_integration_add_entry($table_integration_array); 00088 } 00089 } 00090 } 00091 00092 return $data; 00093 } 00094 00106 function tripal_feature_views_handlers() { 00107 return array( 00108 'info' => array( 00109 'path' => drupal_get_path('module', 'tripal_feature') . '/views_handlers', 00110 ), 00111 'handlers' => array( 00112 'views_handler_field_residues' => array( 00113 'parent' => 'views_handler_field', 00114 ), 00115 ), 00116 ); 00117 } 00118 00122 function tripal_feature_views_data_alter(&$data) { 00123 00124 if ( !(is_array($db_url) and array_key_exists('chado', $db_url)) ) { 00125 00126 // Add featuer relationship to node 00127 $data['node']['feature_chado_nid'] = array( 00128 'group' => 'Feature', 00129 'title' => 'Feature Node', 00130 'help' => 'Links Chado Feature Fields/Data to the Nodes in the current View.', 00131 'real field' => 'nid', 00132 'relationship' => array( 00133 'handler' => 'views_handler_relationship', 00134 'title' => t('Node => Chado'), 00135 'label' => t('Node => Chado'), 00136 'real field' => 'nid', 00137 'base' => 'chado_feature', 00138 'base field' => 'nid' 00139 ), 00140 ); 00141 } 00142 00143 } 00144 00149 function tripal_feature_views_default_views() { 00150 $views = array(); 00151 00152 if (!module_exists('tripal_views')) { 00153 return $views; 00154 } 00155 00156 // Main default view 00157 $view = new view; 00158 $view->name = 'feature_listing'; 00159 $view->description = 'A listing of chado sequence features.'; 00160 $view->tag = 'chado default'; 00161 $view->base_table = 'feature'; 00162 $view->core = 0; 00163 $view->api_version = '2'; 00164 $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */ 00165 $handler = $view->new_display('default', 'features_all', 'default'); 00166 $handler->override_option('fields', array( 00167 'uniquename' => array( 00168 'label' => 'Unique Name', 00169 'alter' => array( 00170 'alter_text' => 0, 00171 'text' => '', 00172 'make_link' => 0, 00173 'path' => 'node/[nid]', 00174 'link_class' => '', 00175 'alt' => '', 00176 'prefix' => '', 00177 'suffix' => '', 00178 'target' => '', 00179 'help' => '', 00180 'trim' => 0, 00181 'max_length' => '', 00182 'word_boundary' => 1, 00183 'ellipsis' => 1, 00184 'html' => 0, 00185 'strip_tags' => 0, 00186 ), 00187 'empty' => '', 00188 'hide_empty' => 0, 00189 'empty_zero' => 0, 00190 'link_to_node' => 0, 00191 'exclude' => 0, 00192 'id' => 'uniquename', 00193 'table' => 'feature', 00194 'field' => 'uniquename', 00195 'relationship' => 'none', 00196 'override' => array( 00197 'button' => 'Override', 00198 ), 00199 ), 00200 'name' => array( 00201 'label' => 'Name', 00202 'alter' => array( 00203 'alter_text' => 0, 00204 'text' => '', 00205 'make_link' => 0, 00206 'path' => '', 00207 'link_class' => '', 00208 'alt' => '', 00209 'prefix' => '', 00210 'suffix' => '', 00211 'target' => '', 00212 'help' => '', 00213 'trim' => 0, 00214 'max_length' => '', 00215 'word_boundary' => 1, 00216 'ellipsis' => 1, 00217 'html' => 0, 00218 'strip_tags' => 0, 00219 ), 00220 'empty' => '', 00221 'hide_empty' => 0, 00222 'empty_zero' => 0, 00223 'link_to_node' => 1, 00224 'exclude' => 0, 00225 'id' => 'name', 00226 'table' => 'feature', 00227 'field' => 'name', 00228 'relationship' => 'none', 00229 'override' => array( 00230 'button' => 'Override', 00231 ), 00232 ), 00233 'name_1' => array( 00234 'label' => 'Type', 00235 'alter' => array( 00236 'alter_text' => 0, 00237 'text' => '', 00238 'make_link' => 0, 00239 'path' => '', 00240 'link_class' => '', 00241 'alt' => '', 00242 'prefix' => '', 00243 'suffix' => '', 00244 'target' => '', 00245 'help' => '', 00246 'trim' => 0, 00247 'max_length' => '', 00248 'word_boundary' => 1, 00249 'ellipsis' => 1, 00250 'html' => 0, 00251 'strip_tags' => 0, 00252 ), 00253 'empty' => '', 00254 'hide_empty' => 0, 00255 'empty_zero' => 0, 00256 'exclude' => 0, 00257 'id' => 'name_1', 00258 'table' => 'cvterm', 00259 'field' => 'name', 00260 'relationship' => 'none', 00261 ), 00262 'common_name' => array( 00263 'label' => 'Common Name', 00264 'alter' => array( 00265 'alter_text' => 0, 00266 'text' => '', 00267 'make_link' => 0, 00268 'path' => '', 00269 'link_class' => '', 00270 'alt' => '', 00271 'prefix' => '', 00272 'suffix' => '', 00273 'target' => '', 00274 'help' => '', 00275 'trim' => 0, 00276 'max_length' => '', 00277 'word_boundary' => 1, 00278 'ellipsis' => 1, 00279 'html' => 0, 00280 'strip_tags' => 0, 00281 ), 00282 'empty' => '', 00283 'hide_empty' => 0, 00284 'empty_zero' => 0, 00285 'link_to_node' => 1, 00286 'exclude' => 0, 00287 'id' => 'common_name', 00288 'table' => 'organism', 00289 'field' => 'common_name', 00290 'relationship' => 'none', 00291 'override' => array( 00292 'button' => 'Override', 00293 ), 00294 ), 00295 'seqlen' => array( 00296 'label' => 'Sequence Length', 00297 'alter' => array( 00298 'alter_text' => 0, 00299 'text' => '', 00300 'make_link' => 0, 00301 'path' => '', 00302 'link_class' => '', 00303 'alt' => '', 00304 'prefix' => '', 00305 'suffix' => '', 00306 'target' => '', 00307 'help' => '', 00308 'trim' => 0, 00309 'max_length' => '', 00310 'word_boundary' => 1, 00311 'ellipsis' => 1, 00312 'html' => 0, 00313 'strip_tags' => 0, 00314 ), 00315 'empty' => '', 00316 'hide_empty' => 0, 00317 'empty_zero' => 0, 00318 'set_precision' => FALSE, 00319 'precision' => 0, 00320 'decimal' => '.', 00321 'separator' => ',', 00322 'prefix' => '', 00323 'suffix' => '', 00324 'exclude' => 0, 00325 'id' => 'seqlen', 00326 'table' => 'feature', 00327 'field' => 'seqlen', 00328 'relationship' => 'none', 00329 ), 00330 'is_obsolete' => array( 00331 'label' => 'Is Obsolete', 00332 'alter' => array( 00333 'alter_text' => 0, 00334 'text' => '', 00335 'make_link' => 0, 00336 'path' => '', 00337 'absolute' => 0, 00338 'link_class' => '', 00339 'alt' => '', 00340 'rel' => '', 00341 'prefix' => '', 00342 'suffix' => '', 00343 'target' => '', 00344 'help' => '', 00345 'trim' => 0, 00346 'max_length' => '', 00347 'word_boundary' => 1, 00348 'ellipsis' => 1, 00349 'html' => 0, 00350 'strip_tags' => 0, 00351 ), 00352 'empty' => '', 00353 'hide_empty' => 0, 00354 'empty_zero' => 0, 00355 'hide_alter_empty' => 1, 00356 'type' => 'separator', 00357 'not' => 0, 00358 'separator' => ', ', 00359 'exclude' => 0, 00360 'id' => 'is_obsolete', 00361 'table' => 'feature', 00362 'field' => 'is_obsolete', 00363 'relationship' => 'none', 00364 ), 00365 'timeaccessioned' => array( 00366 'label' => 'Accessioned On', 00367 'alter' => array( 00368 'alter_text' => 0, 00369 'text' => '', 00370 'make_link' => 0, 00371 'path' => '', 00372 'absolute' => 0, 00373 'link_class' => '', 00374 'alt' => '', 00375 'rel' => '', 00376 'prefix' => '', 00377 'suffix' => '', 00378 'target' => '', 00379 'help' => '', 00380 'trim' => 0, 00381 'max_length' => '', 00382 'word_boundary' => 1, 00383 'ellipsis' => 1, 00384 'html' => 0, 00385 'strip_tags' => 0, 00386 ), 00387 'empty' => '', 00388 'hide_empty' => 0, 00389 'empty_zero' => 0, 00390 'hide_alter_empty' => 1, 00391 'date_format' => 'large', 00392 'custom_date_format' => '', 00393 'type' => 'separator', 00394 'separator' => ', ', 00395 'exclude' => 0, 00396 'id' => 'timeaccessioned', 00397 'table' => 'feature', 00398 'field' => 'timeaccessioned', 00399 'relationship' => 'none', 00400 ), 00401 )); 00402 $handler->override_option('sorts', array( 00403 'common_name' => array( 00404 'order' => 'ASC', 00405 'id' => 'common_name', 00406 'table' => 'organism', 00407 'field' => 'common_name', 00408 'relationship' => 'none', 00409 ), 00410 'name' => array( 00411 'order' => 'ASC', 00412 'id' => 'name', 00413 'table' => 'cvterm', 00414 'field' => 'name', 00415 'relationship' => 'none', 00416 ), 00417 'name_1' => array( 00418 'order' => 'ASC', 00419 'id' => 'name_1', 00420 'table' => 'feature', 00421 'field' => 'name', 00422 'relationship' => 'none', 00423 ), 00424 )); 00425 $handler->override_option('filters', array( 00426 'common_name' => array( 00427 'operator' => '=', 00428 'value' => array(), 00429 'group' => '0', 00430 'exposed' => TRUE, 00431 'expose' => array( 00432 'use_operator' => 0, 00433 'operator' => 'common_name_op', 00434 'identifier' => 'organism', 00435 'label' => 'Organism Common Name', 00436 'remember' => 0, 00437 ), 00438 'case' => 1, 00439 'id' => 'common_name', 00440 'table' => 'organism', 00441 'field' => 'common_name', 00442 'relationship' => 'none', 00443 'values_form_type' => 'select', 00444 'multiple' => 1, 00445 'optional' => 0, 00446 'override' => array( 00447 'button' => 'Override', 00448 ), 00449 'agg' => array( 00450 'records_with' => 1, 00451 'aggregates_with' => 1, 00452 ), 00453 ), 00454 'type_id' => array( 00455 'operator' => '=', 00456 'value' => array(), 00457 'group' => '0', 00458 'exposed' => TRUE, 00459 'expose' => array( 00460 'use_operator' => 0, 00461 'operator' => 'type_id_op', 00462 'identifier' => 'type_id', 00463 'label' => 'Type', 00464 'remember' => 0, 00465 ), 00466 'case' => 1, 00467 'id' => 'type_id', 00468 'table' => 'feature', 00469 'field' => 'type_id', 00470 'relationship' => 'none', 00471 'values_form_type' => 'select', 00472 'multiple' => 1, 00473 'optional' => 0, 00474 'show_all' => 0, 00475 'agg' => array( 00476 'records_with' => 1, 00477 'aggregates_with' => 1, 00478 ), 00479 ), 00480 'name_1' => array( 00481 'operator' => 'allwords', 00482 'value' => '', 00483 'group' => '0', 00484 'exposed' => TRUE, 00485 'expose' => array( 00486 'use_operator' => 0, 00487 'operator' => 'name_1_op', 00488 'identifier' => 'name', 00489 'label' => 'Name Contains', 00490 'bef_filter_description' => '', 00491 'remember' => 0, 00492 ), 00493 'case' => 0, 00494 'id' => 'name_1', 00495 'table' => 'feature', 00496 'field' => 'name', 00497 'relationship' => 'none', 00498 'agg' => array( 00499 'records_with' => 1, 00500 'aggregates_with' => 1, 00501 ), 00502 ), 00503 'search_results' => array( 00504 'operator' => '=', 00505 'value' => '', 00506 'group' => '0', 00507 'exposed' => FALSE, 00508 'expose' => array( 00509 'operator' => FALSE, 00510 'label' => '', 00511 ), 00512 'id' => 'search_results', 00513 'table' => 'views', 00514 'field' => 'search_results', 00515 'relationship' => 'none', 00516 'apply_button' => 'Show', 00517 'no_results_text' => 'Click "Show" to see a list of all features matching the entered criteria. If you leave a any of the criteria blank then the features will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all features will be listed.', 00518 ), 00519 )); 00520 $handler->override_option('access', array( 00521 'type' => 'perm', 00522 'perm' => 'access chado_feature content', 00523 )); 00524 $handler->override_option('cache', array( 00525 'type' => 'none', 00526 )); 00527 $handler->override_option('title', 'Sequence Features'); 00528 $handler->override_option('header', 'Click "Show" to see a list of all features matching the entered criteria. If you leave a any of the criteria blank then the features will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all features will be listed.'); 00529 $handler->override_option('header_format', '2'); 00530 $handler->override_option('header_empty', 0); 00531 $handler->override_option('empty', 'No features matched the supplied criteria.'); 00532 $handler->override_option('empty_format', '2'); 00533 $handler->override_option('items_per_page', 50); 00534 $handler->override_option('use_pager', '1'); 00535 $handler->override_option('style_plugin', 'table'); 00536 $handler->override_option('style_options', array( 00537 'grouping' => '', 00538 'override' => 1, 00539 'sticky' => 0, 00540 'order' => 'asc', 00541 'columns' => array( 00542 'accession' => 'accession', 00543 'accession_link' => 'accession_link', 00544 'name' => 'name', 00545 'uniquename' => 'uniquename', 00546 'name_1' => 'name_1', 00547 'common_name' => 'common_name', 00548 'seqlen' => 'seqlen', 00549 'is_obsolete' => 'is_obsolete', 00550 'is_analysis' => 'is_analysis', 00551 'nid' => 'nid', 00552 ), 00553 'info' => array( 00554 'accession' => array( 00555 'sortable' => 1, 00556 'separator' => '', 00557 ), 00558 'accession_link' => array( 00559 'sortable' => 1, 00560 'separator' => '', 00561 ), 00562 'name' => array( 00563 'sortable' => 1, 00564 'separator' => '', 00565 ), 00566 'uniquename' => array( 00567 'sortable' => 1, 00568 'separator' => '', 00569 ), 00570 'name_1' => array( 00571 'sortable' => 1, 00572 'separator' => '', 00573 ), 00574 'common_name' => array( 00575 'sortable' => 1, 00576 'separator' => '', 00577 ), 00578 'seqlen' => array( 00579 'sortable' => 1, 00580 'separator' => '', 00581 ), 00582 'is_obsolete' => array( 00583 'sortable' => 1, 00584 'separator' => '', 00585 ), 00586 'is_analysis' => array( 00587 'sortable' => 1, 00588 'separator' => '', 00589 ), 00590 'nid' => array( 00591 'separator' => '', 00592 ), 00593 ), 00594 'default' => '-1', 00595 )); 00596 $default_handler = $handler; 00597 $handler = $view->new_display('page', 'Page', 'page_1'); 00598 $handler->override_option('path', 'chado/features'); 00599 $handler->override_option('menu', array( 00600 'type' => 'normal', 00601 'title' => 'Features', 00602 'description' => 'A feature is a biological sequence or a section of a biological sequence, or a collection of such sections. Examples include genes, exons, transcripts, regulatory regions, polypeptides, protein domains, chromosome sequences, sequence variations, cross-genome match regions such as hits and HSPs and so on.', 00603 'weight' => '10', 00604 'name' => 'navigation', 00605 )); 00606 $handler->override_option('tab_options', array( 00607 'type' => 'none', 00608 'title' => '', 00609 'description' => '', 00610 'weight' => 0, 00611 'name' => 'navigation', 00612 )); 00613 // Add code specific to a local chado installation 00614 // NOTE: Edit $handler above to $default_handler for the default display 00615 if (tripal_core_chado_schema_exists()) { 00616 // Add nid field 00617 $fields = $view->get_items('field', 'default'); 00618 $new_fields = array( 00619 'nid' => array( 00620 'label' => 'Nid', 00621 'alter' => array( 00622 'alter_text' => 0, 00623 'text' => '', 00624 'make_link' => 0, 00625 'path' => '', 00626 'absolute' => 0, 00627 'link_class' => '', 00628 'alt' => '', 00629 'rel' => '', 00630 'prefix' => '', 00631 'suffix' => '', 00632 'target' => '', 00633 'help' => '', 00634 'trim' => 0, 00635 'max_length' => '', 00636 'word_boundary' => 1, 00637 'ellipsis' => 1, 00638 'html' => 0, 00639 'strip_tags' => 0, 00640 ), 00641 'empty' => '', 00642 'hide_empty' => 0, 00643 'empty_zero' => 0, 00644 'hide_alter_empty' => 1, 00645 'link_to_node' => 0, 00646 'exclude' => 1, 00647 'id' => 'nid', 00648 'table' => 'node', 00649 'field' => 'nid', 00650 'relationship' => 'none', 00651 ) 00652 ); 00653 $fields = $new_fields + $fields; 00654 // Adds feature => Node relationship 00655 $default_handler->override_option('relationships', array( 00656 'nid' => array( 00657 'label' => 'Feature to Node', 00658 'required' => 0, 00659 'id' => 'nid', 00660 'table' => 'chado_feature', 00661 'field' => 'nid', 00662 'relationship' => 'none', 00663 ), 00664 )); 00665 // Change analysis.name to have a link to the node 00666 $fields['name']['alter']['link_to_node'] = 1; 00667 $default_handler->override_option('fields', $fields); 00668 // Only show records with published nodes 00687 } 00688 $views[$view->name] = $view; 00689 00690 return $views; 00691 }