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Release 1.3.1

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1 parent 8b5e9ff commit e417e64a4cc7bba5057dec488cee86aa54432170 Johannes Goll committed Oct 12, 2011
Showing with 68,961 additions and 141,008 deletions.
  1. +1 −1 README
  2. +4 −3 app/config/constants.php
  3. +1 −1 app/config/core.php
  4. +2 −1 app/controllers/app_controller.php
  5. +28 −23 app/controllers/browse_controller.php
  6. +976 −0 app/controllers/browse_controller_apis.php
  7. +181 −43 app/controllers/compare_controller.php
  8. +3 −3 app/controllers/components/matrix.php
  9. +45 −30 app/controllers/components/r.php
  10. +230 −1 app/controllers/components/solr.php
  11. +1 −0 app/controllers/dashboard_controller.php
  12. +322 −0 app/controllers/itol_controller.php
  13. +3 −0 app/controllers/populations_controller.php
  14. +1 −1 app/controllers/projects_controller.php
  15. +106 −7 app/controllers/search_controller.php
  16. +23 −16 app/controllers/view_controller.php
  17. +1 −2 app/models/go_graph.php
  18. +5 −6 app/models/go_term.php
  19. +4 −2 app/models/pathway.php
  20. +27 −10 app/models/project.php
  21. +2 −2 app/models/taxonomy.php
  22. +53 −0 app/models/taxonomy_apis.php
  23. +8 −7 app/views/compare/index.ctp
  24. +15 −20 app/views/compare/result_panel.ctp
  25. +1 −1 app/views/compare/tab_panel.ctp
  26. +15 −29 app/views/helpers/matrix.php
  27. +7 −1 app/views/menus/quick.ctp
  28. +7 −4 app/views/projects/view.ctp
  29. +19 −2 app/views/search/index.ctp
  30. +31 −0 app/webroot/css/search_dataset.css
  31. +2 −0 app/webroot/css/view.css
  32. +3 −3 app/webroot/js/michael-multiselect-2a0569f/css/ui.multiselect.css
  33. +4 −4 app/webroot/js/michael-multiselect-2a0569f/js/ui.multiselect.large.js
  34. BIN mysql/gene_ontology_mysql_dump.sql → app/webroot/sequence.db
  35. +2 −0 cake/libs/model/datasources/dbo/dbo_mysql.php
  36. +762 −636 cake/libs/model/datasources/dbo/dbo_sqlite3.php
  37. +2 −0 cake/libs/model/datasources/dbo_source.php
  38. +10,511 −26,306 data/xml/HOT01-0010M.xml
  39. +13,429 −29,386 data/xml/HOT02-0070M.xml
  40. +8,211 −15,705 data/xml/HOT03-0130M.xml
  41. +9,679 −20,410 data/xml/HOT04-0200M.xml
  42. +3,287 −3,233 data/xml/HOT05-0500M.xml
  43. +15,269 −39,616 data/xml/HOT06-0770M.xml
  44. +4,067 −4,080 data/xml/HOT07-4000M.xml
  45. +10 −0 db/README
  46. +386 −153 mysql/metarep_mysql_dump.sql → db/metarep.mysql.db
  47. BIN db/metarep.sqlite3.db
  48. +71 −77 scripts/perl/metarep_loader.pl
  49. +3 −3 solr/conf/schema.xml
  50. +0 −24 solr/conf/scripts.conf
  51. +45 −102 solr/conf/solrconfig.xml
  52. +1,072 −1,046 solr/conf/solrconfig_slave.xml
  53. +11 −0 solr/conf/solrlog.properties
  54. +0 −1 solr/conf/stopwords.txt
  55. +11 −5 vendors/SolrPhpClient_r53/Apache/Solr/HttpTransport/CurlNoReuse.php
  56. +1 −1 vendors/SolrPhpClient_r53/Apache/Solr/Service.php
  57. +1 −1 vendors/SolrPhpClient_r53/Apache/Solr/Service/Balancer.php
View
2 README
@@ -5,7 +5,7 @@ METAREP DIRECTORIES
/data example dataset*
/scripts perl and R scripts
/doc documentation
-/mysql mysql database dump
+/db relational databases
/solr solr/lucene configuration files
/vendors 3rd-party php tools
View
@@ -36,13 +36,14 @@
define('FISHER', 0);
define('ABSOLUTE_COUNTS', 1);
define('RELATIVE_COUNTS', 2);
-define('HEATMAP', 3);
+define('HEATMAP_COUNTS', 3);
define('CHISQUARE', 4);
define('WILCOXON', 5);
define('METASTATS', 6);
define('HIERARCHICAL_CLUSTER_PLOT', 7);
define('MDS_PLOT', 8);
define('HEATMAP_PLOT', 9);
+define('MOSAIC_PLOT', 10);
//define compare dataset mode
define('SHOW_ALL_DATASETS',0);
@@ -96,6 +97,6 @@
define('HEATMAP_GREEN_START', '31A354');
define('HEATMAP_GREEN_END', 'E5F5E0');
-define('PHP_HTTP_TRANSPORT_CURL_REUSE', 'CURL_REUSE');
+define('PHP_HTTP_TRANSPORT_CURL_REUSE', 'CURL_NO_REUSE');
define('PHP_HTTP_TRANSPORT_CURL_NOREUSE', 'CURL_NO_REUSE');
-define('PHP_HTTP_TRANSPORT_FILE_GET_CONTENTS', 'FILE_GET_CONTENTS');
+define('PHP_HTTP_TRANSPORT_FILE_GET_CONTENTS', 'FILE_GET_CONTENTS');
View
@@ -47,7 +47,7 @@
* In development mode, you need to click the flash message to continue.
*/
- Configure::write('debug', '1');
+ Configure::write('debug', '0');
/**
* Application wide charset encoding
@@ -30,7 +30,7 @@ class AppController extends Controller {
//treated with caution. It caused a chache exception and returned imcomplete
//model objects google"$persistModel cakephp incomplete object". Setting this to false
//until the root cause for this exception has been identified.
- var $persistModel = false;
+ var $persistModel = true;
var $helpers = array('Session','Html', 'Form','Javascript','Ajax');
var $components = array('Session','Cookie','RequestHandler','Authsome' => array('model' => 'User'));
@@ -71,6 +71,7 @@ class AppController extends Controller {
'search/count',
'search/dowloadFacets',
'search/dowloadData',
+ 'search/dowloadSequences',
'search/link',
'browse/blastTaxonomy',
'browse/apisTaxonomy',
@@ -66,9 +66,10 @@ function blastTaxonomy($dataset,$expandTaxon=1,$query='*:*') {
$this->loadModel('Taxonomy');
$this->pageTitle = 'Browse Taxonomy (Blast)';
- $pipeline = $this->Project->getPipeline($dataset);
+ $pipeline = $this->Project->getPipeline($dataset);
+ $optionalDatatypes = $this->Project->checkOptionalDatatypes(array($dataset));
- if($pipeline === 'HUMANN') {
+ if($pipeline === PIPELINE_HUMANN || $optionalDatatypes['ko']) {
$this->facetFields = array(
'blast_species'=>'Species (Blast)',
'ko_id'=>'Kegg Ortholog',
@@ -185,17 +186,18 @@ function apisTaxonomy($dataset,$expandTaxon=1,$query='*:*') {
$this->loadModel('Project');
$this->loadModel('Taxonomy');
$this->pageTitle = 'Browse Taxonomy (Apis)';
-
- $pipeline = $this->Project->getPipeline($dataset);
- if($pipeline === 'HUMANN') {
+ $pipeline = $this->Project->getPipeline($dataset);
+ $optionalDatatypes = $this->Project->checkOptionalDatatypes(array($dataset));
+
+ if($pipeline === PIPELINE_HUMANN || $optionalDatatypes['ko']) {
$this->facetFields = array(
'blast_species'=>'Species (Blast)',
'ko_id'=>'Kegg Ortholog',
'go_id'=>'Gene Ontology',
'ec_id'=>'Enzyme',
);
- }
+ }
if($this->Session->check($function.'.browse.query')){
$query = $this->Session->read($function.'.browse.query');
@@ -307,16 +309,17 @@ function enzymes($dataset,$expandTaxon='root',$query = '*:*') {
$this->loadModel('Enzymes');
$this->pageTitle = 'Browse Enzymes';
- $pipeline = $this->Project->getPipeline($dataset);
+ $pipeline = $this->Project->getPipeline($dataset);
+ $optionalDatatypes = $this->Project->checkOptionalDatatypes(array($dataset));
- if($pipeline === 'HUMANN') {
+ if($pipeline === PIPELINE_HUMANN || $optionalDatatypes['ko']) {
$this->facetFields = array(
'blast_species'=>'Species (Blast)',
'ko_id'=>'Kegg Ortholog',
'go_id'=>'Gene Ontology',
'ec_id'=>'Enzyme',
);
- }
+ }
if($this->Session->check($function.'.browse.query')){
$query = $this->Session->read($function.'.browse.query');
@@ -427,16 +430,17 @@ function geneOntology($dataset,$expandTaxon='root',$query='*:*') {
$this->loadModel('GoGraph');
$this->pageTitle = 'Browse Gene Ontology';
- $pipeline = $this->Project->getPipeline($dataset);
+ $pipeline = $this->Project->getPipeline($dataset);
+ $optionalDatatypes = $this->Project->checkOptionalDatatypes(array($dataset));
- if($pipeline === 'HUMANN') {
+ if($pipeline === PIPELINE_HUMANN || $optionalDatatypes['ko']) {
$this->facetFields = array(
'blast_species'=>'Species (Blast)',
'ko_id'=>'Kegg Ortholog',
'go_id'=>'Gene Ontology',
'ec_id'=>'Enzyme',
);
- }
+ }
if($this->Session->check($function.'.browse.query')){
$query = $this->Session->read($function.'.browse.query');
@@ -656,15 +660,16 @@ private function pathways($dataset,$parentId,$query,$pathwayModel) {
$function = $this->underscoreToCamelCase($pathwayModel);
- $pipeline = $this->Project->getPipeline($dataset);
-
- if($pipeline === PIPELINE_HUMANN) {
- $this->facetFields = array(
- 'blast_species'=>'Species (Blast)',
- 'ko_id'=>'Kegg Ortholog',
- 'go_id'=>'Gene Ontology',
- 'ec_id'=>'Enzyme',
- );
+ $pipeline = $this->Project->getPipeline($dataset);
+ $optionalDatatypes = $this->Project->checkOptionalDatatypes(array($dataset));
+
+ if($pipeline === PIPELINE_HUMANN || $optionalDatatypes['ko']) {
+ $this->facetFields = array(
+ 'blast_species'=>'Species (Blast)',
+ 'ko_id'=>'Kegg Ortholog',
+ 'go_id'=>'Gene Ontology',
+ 'ec_id'=>'Enzyme',
+ );
}
//initialize variables
@@ -875,7 +880,7 @@ public function downloadChildCounts($dataset,$node,$mode,$numHits,$query = "*:*"
$content = $this->Format->infoString("Browse $mode Results",$dataset,$query,0,$numHits,$node);
$content.=$this->Format->facetToDownloadString($node,$childCounts,$numHits);
- $fileName = "jcvi_metagenomics_report_".time().'.txt';
+ $fileName = uniqid('jcvi_metagenomics_report_').'.txt';
header("Content-type: text/plain");
header("Content-Disposition: attachment;filename=$fileName");
@@ -916,7 +921,7 @@ public function dowloadFacets($dataset,$node,$mode,$numHits,$query = "*:*") {
#die("Browse $mode Results - Top 10 Functional Categories,$dataset,$facets,$query,$numHits,$node");
$content=$this->Format->facetListToDownloadString("Browse $mode Results - Top 10 Functional Categories",$dataset,$facets,$facetFields,$query,$numHits,$node);
- $fileName = "jcvi_metagenomics_report_".time().'.txt';
+ $fileName = uniqid('jcvi_metagenomics_report_').'.txt';
header("Content-type: text/plain");
header("Content-Disposition: attachment;filename=$fileName");
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