Procházet zdrojové kódy

Merge branch '7.x-2.x' of git.drupal.org:sandbox/spficklin/1337878 into 7.x-2.x

Lacey Sanderson před 11 roky
rodič
revize
80cffe0da2
100 změnil soubory, kde provedl 113 přidání a 191 odebrání
  1. 0 7
      tripal_analysis/theme/css/tripal_analysis.css
  2. 1 1
      tripal_analysis/theme/tripal_analysis/tripal_analysis_base.tpl.php
  3. 1 1
      tripal_analysis/theme/tripal_analysis/tripal_analysis_properties.tpl.php
  4. 2 2
      tripal_analysis/tripal_analysis.info
  5. 1 2
      tripal_analysis/tripal_analysis.module
  6. 1 1
      tripal_bulk_loader/theme/node--tripal-bulk-loader.tpl.php
  7. 1 1
      tripal_bulk_loader/theme/tripal_bulk_loader_template.tpl.php
  8. 2 2
      tripal_bulk_loader/tripal_bulk_loader.info
  9. 0 7
      tripal_contact/theme/css/tripal_contact.css
  10. 0 0
      tripal_contact/theme/js/tripal_contact.js
  11. 1 1
      tripal_contact/theme/tripal_contact/tripal_contact_base.tpl.php
  12. 1 1
      tripal_contact/theme/tripal_contact/tripal_contact_properties.tpl.php
  13. 1 1
      tripal_contact/theme/tripal_contact/tripal_contact_publications.tpl.php
  14. 1 1
      tripal_contact/theme/tripal_contact/tripal_contact_relationships.tpl.php
  15. 2 2
      tripal_contact/tripal_contact.info
  16. 0 2
      tripal_contact/tripal_contact.module
  17. 4 4
      tripal_core/theme/css/tripal.css
  18. 8 3
      tripal_core/tripal_core.info
  19. 0 5
      tripal_core/tripal_core.module
  20. 2 2
      tripal_cv/tripal_cv.info
  21. 0 0
      tripal_db/theme/css/tripal_db.css
  22. 0 0
      tripal_db/theme/js/tripal_db.js
  23. 2 2
      tripal_db/tripal_db.info
  24. 0 3
      tripal_db/tripal_db.module
  25. 0 37
      tripal_feature/theme/css/tripal_feature.css
  26. 1 1
      tripal_feature/theme/tripal_feature/tripal_feature_alignments.tpl.php
  27. 1 1
      tripal_feature/theme/tripal_feature/tripal_feature_analyses.tpl.php
  28. 1 1
      tripal_feature/theme/tripal_feature/tripal_feature_base.tpl.php
  29. 1 1
      tripal_feature/theme/tripal_feature/tripal_feature_featurepos.tpl.php
  30. 1 1
      tripal_feature/theme/tripal_feature/tripal_feature_publications.tpl.php
  31. 1 1
      tripal_feature/theme/tripal_feature/tripal_feature_references.tpl.php
  32. 1 1
      tripal_feature/theme/tripal_feature/tripal_feature_relationships.tpl.php
  33. 1 1
      tripal_feature/theme/tripal_feature/tripal_feature_sequence.tpl.php
  34. 1 1
      tripal_feature/theme/tripal_feature/tripal_feature_synonyms.tpl.php
  35. 1 1
      tripal_feature/theme/tripal_feature/tripal_feature_terms.tpl.php
  36. 1 1
      tripal_feature/theme/tripal_organism/tripal_organism_feature_browser.tpl.php
  37. 2 2
      tripal_feature/theme/tripal_organism/tripal_organism_feature_counts.tpl.php
  38. 5 4
      tripal_feature/tripal_feature.info
  39. 1 2
      tripal_feature/tripal_feature.module
  40. 0 7
      tripal_featuremap/theme/css/tripal_featuremap.css
  41. 0 0
      tripal_featuremap/theme/js/tripal_featuremap.js
  42. 1 1
      tripal_featuremap/theme/tripal_featuremap/tripal_featuremap_base.tpl.php
  43. 1 1
      tripal_featuremap/theme/tripal_featuremap/tripal_featuremap_featurepos.tpl.php
  44. 0 0
      tripal_featuremap/theme/tripal_featuremap/tripal_featuremap_properties.tpl.php
  45. 1 1
      tripal_featuremap/theme/tripal_featuremap/tripal_featuremap_publication.tpl.php
  46. 1 1
      tripal_featuremap/theme/tripal_featuremap/tripal_featuremap_references.tpl.php
  47. 0 0
      tripal_featuremap/theme/tripal_featuremap/tripal_featuremap_teaser.tpl.php
  48. 0 0
      tripal_featuremap/theme/tripal_featuremap_help.tpl.php
  49. 2 4
      tripal_featuremap/tripal_featuremap.info
  50. 8 9
      tripal_featuremap/tripal_featuremap.module
  51. 0 0
      tripal_genetic/theme/css/tripal_genetic.css
  52. 0 0
      tripal_genetic/theme/js/tripal_genetic.js
  53. 1 1
      tripal_genetic/theme/tripal_feature/tripal_feature_genotypes.tpl.php
  54. 0 0
      tripal_genetic/theme/tripal_genetic.help.tpl.php
  55. 0 0
      tripal_genetic/theme/tripal_genetic_help.tpl.php
  56. 1 1
      tripal_genetic/theme/tripal_stock/tripal_stock_genotypes.tpl.php
  57. 2 2
      tripal_genetic/tripal_genetic.info
  58. 3 3
      tripal_genetic/tripal_genetic.module
  59. 0 0
      tripal_library/theme/css/tripal_library.css
  60. 0 0
      tripal_library/theme/js/tripal_library.js
  61. 1 1
      tripal_library/theme/tripal_feature/tripal_feature_libraries.tpl.php
  62. 1 1
      tripal_library/theme/tripal_library/tripal_library_base.tpl.php
  63. 0 0
      tripal_library/theme/tripal_library/tripal_library_properties.tpl.php
  64. 1 1
      tripal_library/theme/tripal_library/tripal_library_publications.tpl.php
  65. 1 1
      tripal_library/theme/tripal_library/tripal_library_references.tpl.php
  66. 1 1
      tripal_library/theme/tripal_library/tripal_library_synonyms.tpl.php
  67. 0 0
      tripal_library/theme/tripal_library/tripal_library_teaser.tpl.php
  68. 1 1
      tripal_library/theme/tripal_library/tripal_library_terms.tpl.php
  69. 0 0
      tripal_library/theme/tripal_library_help.tpl.php
  70. 1 1
      tripal_library/theme/tripal_organism/tripal_organism_libraries.tpl.php
  71. 2 4
      tripal_library/tripal_library.info
  72. 10 10
      tripal_library/tripal_library.module
  73. 0 0
      tripal_natural_diversity/theme/css/tripal_natural_diversity.css
  74. 0 0
      tripal_natural_diversity/theme/js/tripal_natural_diversity.js
  75. 1 1
      tripal_natural_diversity/theme/tripal_feature/tripal_feature_nd_genotypes.tpl.php
  76. 0 0
      tripal_natural_diversity/theme/tripal_natural_diversity_help.tpl.php
  77. 1 1
      tripal_natural_diversity/theme/tripal_stock/tripal_stock_nd_genotypes.tpl.php
  78. 1 1
      tripal_natural_diversity/theme/tripal_stock/tripal_stock_nd_phenotypes.tpl.php
  79. 2 2
      tripal_natural_diversity/tripal_natural_diversity.info
  80. 4 4
      tripal_natural_diversity/tripal_natural_diversity.module
  81. 0 4
      tripal_organism/theme/css/tripal_organism.css
  82. 0 0
      tripal_organism/theme/js/tripal_organism.js
  83. 1 1
      tripal_organism/theme/tripal_organism/tripal_organism_base.tpl.php
  84. 1 1
      tripal_organism/theme/tripal_organism/tripal_organism_references.tpl.php
  85. 2 4
      tripal_organism/tripal_organism.info
  86. 0 3
      tripal_organism/tripal_organism.module
  87. 0 0
      tripal_phenotype/theme/css/tripal_phenotype.css
  88. 0 0
      tripal_phenotype/theme/js/tripal_phenotype.js
  89. 1 1
      tripal_phenotype/theme/tripal_feature/tripal_feature_phenotypes.tpl.php
  90. 0 0
      tripal_phenotype/theme/tripal_phenotype_help.tpl.php
  91. 2 2
      tripal_phenotype/tripal_phenotype.info
  92. 2 2
      tripal_phenotype/tripal_phenotype.module
  93. 0 0
      tripal_project/theme/css/tripal_project.css
  94. 0 0
      tripal_project/theme/js/tripal_project.js
  95. 1 1
      tripal_project/theme/tripal_project/tripal_project_base.tpl.php
  96. 1 1
      tripal_project/theme/tripal_project/tripal_project_contact.tpl.php
  97. 1 1
      tripal_project/theme/tripal_project/tripal_project_properties.tpl.php
  98. 1 1
      tripal_project/theme/tripal_project/tripal_project_publications.tpl.php
  99. 1 1
      tripal_project/theme/tripal_project/tripal_project_relationships.tpl.php
  100. 0 0
      tripal_project/theme/tripal_project/tripal_project_teaser.tpl.php

+ 0 - 7
tripal_analysis/theme/css/tripal_analysis.css

@@ -1,7 +0,0 @@
-#tripal-analysis-edit-properties-table {
-  width: auto;
-}
-
-#tripal-analysis-edit-properties-table .form-item {
-  white-space: normal;
-}

+ 1 - 1
tripal_analysis/theme/tripal_analysis/tripal_analysis_base.tpl.php

@@ -2,7 +2,7 @@
 $analysis = $variables['node']->analysis;
 $analysis = tripal_core_expand_chado_vars($analysis,'field','analysis.description'); ?>
 
-<div class="tripal__analysis-info-box-desc tripal-info-box-desc"></div><?php 
+<div class="tripal__analysis-data-block-desc tripal-data-block-desc"></div><?php 
   
 // the $headers array is an array of fields to use as the colum headers. 
 // additional documentation can be found here 

+ 1 - 1
tripal_analysis/theme/tripal_analysis/tripal_analysis_properties.tpl.php

@@ -6,7 +6,7 @@ $analysis = tripal_core_expand_chado_vars($analysis,'table', 'analysisprop', arr
 $properties = $analysis->analysisprop;
 
 if (count($properties) > 0) { ?>
-  <div class="tripal_analysis-info-box-desc tripal-info-box-desc">Additional information about this analysis:</div><?php
+  <div class="tripal_analysis-data-block-desc tripal-data-block-desc">Additional information about this analysis:</div><?php
   
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here

+ 2 - 2
tripal_analysis/tripal_analysis.info

@@ -1,9 +1,9 @@
 name = Tripal Analysis
-description = A module for interfacing organisms from the GMOD chado database with Drupal. It provides viewing, inserting and editing of organisms.
+description = Supports the companalyses tables of Chado by providing pages for viewing and editing of analyses. Table list at: http://gmod.org/wiki/Chado_Companalysis_Module.
 core = 7.x
 project = tripal_analysis
 package = Tripal
-version = 7.x-2.0-beta1
+version = 7.x-2.0a
 configure = admin/tripal/chado/tripal_analysis/configuration
 
 dependencies[] = tripal_core

+ 1 - 2
tripal_analysis/tripal_analysis.module

@@ -29,8 +29,7 @@ require_once 'includes/tripal_analysis.chado_node.inc';
  * @ingroup tripal_analysis
  */
 function tripal_analysis_init() {
-  drupal_add_js(drupal_get_path('module', 'tripal_analysis') . '/theme/js/tripal_analysis.js');
-  drupal_add_css(drupal_get_path('module', 'tripal_analysis') . '/theme/css/tripal_analysis.css');
+
 }
 
 

+ 1 - 1
tripal_bulk_loader/theme/node--tripal-bulk-loader.tpl.php

@@ -2,7 +2,7 @@
   <div class="tripal_bulk_loader-info-box-title tripal-info-box-title">
     <?php if ($teaser) { print l($node->title, 'node/'.$node->nid); } ?>
   </div>
-  <div class="tripal_bulk_loader-info-box-desc tripal-info-box-desc"></div>
+  <div class="tripal_bulk_loader-data-block-desc tripal-data-block-desc"></div>
 
   <table id="tripal_bulk_loader-base-table" class="tripal_bulk_loader-table tripal-table tripal-table-vert">
     <tr class="tripal_bulk_loader-table-odd-row tripal-table-odd-row">

+ 1 - 1
tripal_bulk_loader/theme/tripal_bulk_loader_template.tpl.php

@@ -37,7 +37,7 @@
 
 <div id="tripal_bulk_loader-base-box" class="tripal_bulk_loader-info-box tripal-info-box">
   <div class="tripal_bulk_loader-info-box-title tripal-info-box-title">Template Description</div>
-  <div class="tripal_bulk_loader-info-box-desc tripal-info-box-desc"></div>
+  <div class="tripal_bulk_loader-data-block-desc tripal-data-block-desc"></div>
 
 <?php if (sizeof($constants)) { ?>
   <table id="tripal_bulk_loader-template_constant-table" class="tripal_bulk_loader-table tripal-table tripal-table-vert">

+ 2 - 2
tripal_bulk_loader/tripal_bulk_loader.info

@@ -1,9 +1,9 @@
 name = Tripal Bulk Loader
-description = A module for uploading tab-delimit data into GMOD chado database using templates.
+description = Supports the construction of templates for customizable uploading of tab-delimited files into the Chado database.
 core = 7.x
 project = tripal_bulk_loader
 package = Tripal
-version = 7.x-2.0-beta1
+version = 7.x-2.0a
 
 dependencies[] = tripal_core
 dependencies[] = tripal_views

+ 0 - 7
tripal_contact/theme/css/tripal_contact.css

@@ -1,7 +0,0 @@
-#tripal-contact-edit-properties-table {
-  width: auto;
-}
-
-#tripal-contact-edit-properties-table .form-item {
-  white-space: normal;
-}

+ 0 - 0
tripal_contact/theme/js/tripal_contact.js


+ 1 - 1
tripal_contact/theme/tripal_contact/tripal_contact_base.tpl.php

@@ -1,7 +1,7 @@
 <?php
 $contact = $variables['node']->contact; ?>
 
-<div class="tripal_contact-info-box-desc tripal-info-box-desc"></div> <?php
+<div class="tripal_contact-data-block-desc tripal-data-block-desc"></div> <?php
 
 // the $headers array is an array of fields to use as the colum headers. 
 // additional documentation can be found here 

+ 1 - 1
tripal_contact/theme/tripal_contact/tripal_contact_properties.tpl.php

@@ -20,7 +20,7 @@ if ($contactprops) {
 
 
 if (count($properties) > 0) { ?>
-  <div class="tripal_contact-info-box-desc tripal-info-box-desc">Additional information about this contact:</div><?php
+  <div class="tripal_contact-data-block-desc tripal-data-block-desc">Additional information about this contact:</div><?php
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here
   // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7

+ 1 - 1
tripal_contact/theme/tripal_contact/tripal_contact_publications.tpl.php

@@ -8,7 +8,7 @@ $pubauthor_contacts = $contact->pubauthor_contact;
 
 
 if (count($pubauthor_contacts) > 0) { ?>
-  <div class="tripal_pubauthor_contact-info-box-desc tripal-info-box-desc"></div> <?php 
+  <div class="tripal_pubauthor_contact-data-block-desc tripal-data-block-desc"></div> <?php 
 
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here

+ 1 - 1
tripal_contact/theme/tripal_contact/tripal_contact_relationships.tpl.php

@@ -23,7 +23,7 @@ $object_rels = $all_relationships['object'];
 $subject_rels = $all_relationships['subject'];
 
 if (count($object_rels) > 0 or count($subject_rels) > 0) { ?>
-  <div class="tripal_contact-info-box-desc tripal-info-box-desc"></div> <?php
+  <div class="tripal_contact-data-block-desc tripal-data-block-desc"></div> <?php
   // first add in the subject relationships.  
   foreach ($subject_rels as $rel_type => $rels){
     foreach ($rels as $obj_type => $objects){ ?>

+ 2 - 2
tripal_contact/tripal_contact.info

@@ -1,9 +1,9 @@
 name = Tripal Contact
-description = A module for interfacing the GMOD chado database with Drupal, providing viewing of contacts such as people, organizations or entities.
+description = Supports the contact tables of Chado by providing pages for viewing and editing of contacts. Table list at: http://gmod.org/wiki/Chado_Contact_Module.
 core = 7.x
 project = tripal_contact
 package = Tripal
-version = 7.x-2.0-beta1
+version = 7.x-2.0a
 
 dependencies[] = tripal_core
 dependencies[] = tripal_views

+ 0 - 2
tripal_contact/tripal_contact.module

@@ -32,8 +32,6 @@ function tripal_contact_views_api() {
  * @ingroup tripal_contact
  */
 function tripal_contact_init() {
-  drupal_add_js(drupal_get_path('module', 'tripal_contact') . '/theme/js/tripal_contact.js');
-  drupal_add_css(drupal_get_path('module', 'tripal_contact') . '/theme/css/tripal_contact.css');
 
 }
 

+ 4 - 4
tripal_core/theme/css/tripal.css

@@ -8,7 +8,7 @@
  * |-----------------------------------------------|
  * |  .tripal-contents                             |
  * | |-------------------------------------------| |
- * | | #tripal-contents-table                    | |
+ * | | .tripal-contents-table                    | |
  * | |        |                                  | |
  * | |        |                                  | |
  * | | TOC    |          Data                    | |
@@ -100,11 +100,11 @@
  * 'tripal-info-box-desc' 
  *
  * |-----------------------------------------------|
- * |  .tripal-info-box                             |
+ * |  .tripal-data-block                           |
  * | |-------------------------------------------| |
- * | | .tripal-info-box-title                    | |
+ * | | .tripal-data-block-title                  | |
  * | |-------------------------------------------| |
- * | | .tripal-info-box-desc                     | |
+ * | | .tripal-data-block-desc                   | |
  * | |-------------------------------------------| |
  * |                                               |
  * | (Block data goes here)                        |

+ 8 - 3
tripal_core/tripal_core.info

@@ -1,9 +1,14 @@
 name = Tripal Core
-description = The core module for the Tripal package that integrates Drupal and GMOD chado. This module provides common support for all Tripal modules.
+description = Provides support for all Tripal modules and includes the Tripal API, jobs management, materialized views, Chado installation and custom tables.
 core = 7.x
 project = tripal_core
 package = Tripal
-version = 7.x-2.0-beta1
+version = 7.x-2.0a
 configure = admin/tripal
 
-dependencies[] = views
+stylesheets[all][] = theme/css/tripal.css
+scripts[]          = theme/js/tripal.js
+
+dependencies[]     = views
+dependencies[]     = path
+dependencies[]     = search

+ 0 - 5
tripal_core/tripal_core.module

@@ -81,11 +81,6 @@ tripal_core_set_globals();
 function tripal_core_init() {
   global $base_url;
 
-  // add javascript files
-  drupal_add_js(drupal_get_path('module', 'tripal_core') . '/theme/js/tripal.js');
-  drupal_add_css(drupal_get_path('module', 'tripal_core') . '/theme/css/tripal.css');
-
-
   // create the 'tripal' controlled volcabulary in chado but only if it doesn't already exist, and
   // only if the chado database is present.
   if ($GLOBALS["chado_is_installed"]) {

+ 2 - 2
tripal_cv/tripal_cv.info

@@ -1,9 +1,9 @@
 name = Tripal CV
-description = The controlled vocabulary module for the Tripal package that integrates Drupal and GMOD chado. This module provides support for managing and viewing controlled vocabularies.
+description = Supports the Controlled Vocabulary (CV) tables of Chado by providing pages for viewing and editing of CVs. Table list at: http://gmod.org/wiki/Chado_CV_Module.
 core = 7.x
 project = tripal_cv
 package = Tripal
-version = 7.x-2.0-beta1
+version = 7.x-2.0a
 configure = admin/tripal/chado/tripal_cv
 
 dependencies[] = tripal_core

+ 0 - 0
tripal_db/theme/css/tripal_db.css


+ 0 - 0
tripal_db/theme/js/tripal_db.js


+ 2 - 2
tripal_db/tripal_db.info

@@ -1,9 +1,9 @@
 name = Tripal DB
-description = The database module for the Tripal package that integrates Drupal and GMOD chado. This module provides support for managing and viewing external databases.
+description = Supports the database cross-reference tables of Chado by providing pages for viewing and editing of databases and their cross-references. Table list at: http://gmod.org/wiki/Chado_General_Module.
 core = 7.x
 project = tripal_db
 package = Tripal
-version = 7.x-2.0-beta1
+version = 7.x-2.0a
 configure = admin/tripal/chado/tripal_db
 
 dependencies[] = tripal_core

+ 0 - 3
tripal_db/tripal_db.module

@@ -21,9 +21,6 @@ require_once "includes/tripal_db.admin.inc";
  */
 function tripal_db_init() {
 
-  // add the tripal_db JS and CSS
-  drupal_add_css(drupal_get_path('module', 'tripal_db') . '/theme/css/tripal_db.css');
-  drupal_add_js(drupal_get_path('module', 'tripal_db') . '/theme/js/tripal_db.js');
 }
 /**
  *

+ 0 - 37
tripal_feature/theme/css/tripal_feature.css

@@ -51,43 +51,6 @@ span.tripal_feature-featureloc_sequence-intron {
    background-image: url('../images/type_color6.png');
  
 }
-/* information tables on the feature pages */
-table.tripal_feature-relationships-subject-table th {
-   background-color: #EEEEEE;
-   text-align: left;
-}
-table.tripal_feature-relationships-object-table th {
-   background-color: #EEEEEE;
-   text-align: left;
-}
-table.tripal_feature-locations-table th {
-   background-color: #EEEEEE;
-   text-align: left;
-}
-table.tripal_feature-references-table th {
-   background-color: #EEEEEE;
-   text-align: left;
-
-}
-/* feature relationship edit form */
-#tripal-feature-edit-ALL-relationships-form .form-item,
-#tripal-feature-edit-ALL-db-references-form .form-item {
-   float: left;
-   margin: 0 10px 0 0;
-   
-}
-#tripal-feature-edit-ALL-db-references-form .form-submit {
-   float: none;
-   display: block;
-}
-.tripal_feature-obsolete {
-   color: red;
-   font-weight: bold;
-   font-style: italic;
-   padding-bottom: 15px; 
-   text-align: center;
-}
-
 
 /* 
  * Sequence Retrieval Form

+ 1 - 1
tripal_feature/theme/tripal_feature/tripal_feature_alignments.tpl.php

@@ -58,7 +58,7 @@ $feature = $variables['node']->feature;
 $alignments = $feature->all_featurelocs;
 
 if(count($alignments) > 0){ ?>
-  <div class="tripal_feature-info-box-desc tripal-info-box-desc">The following features are aligned</div><?php
+  <div class="tripal_feature-data-block-desc tripal-data-block-desc">The following features are aligned</div><?php
   
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here

+ 1 - 1
tripal_feature/theme/tripal_feature/tripal_feature_analyses.tpl.php

@@ -6,7 +6,7 @@ $analyses = $feature->analysisfeature;
 
 // don't show this page if there are no analyses
 if (count($analyses) > 0) { ?>
-  <div class="tripal_feature-info-box-desc tripal-info-box-desc">This <?php print $feature->type_id->name ?> is derived from or has results from the following analyses</div> <?php
+  <div class="tripal_feature-data-block-desc tripal-data-block-desc">This <?php print $feature->type_id->name ?> is derived from or has results from the following analyses</div> <?php
   
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here

+ 1 - 1
tripal_feature/theme/tripal_feature/tripal_feature_base.tpl.php

@@ -1,7 +1,7 @@
 <?php
 $feature  = $variables['node']->feature;  ?>
 
-<div class="tripal_feature-info-box-desc tripal-info-box-desc"></div> <?php
+<div class="tripal_feature-data-block-desc tripal-data-block-desc"></div> <?php
  
 // the $headers array is an array of fields to use as the colum headers. 
 // additional documentation can be found here 

+ 1 - 1
tripal_feature/theme/tripal_feature/tripal_feature_featurepos.tpl.php

@@ -39,7 +39,7 @@ $total_records = $_SESSION['chado_pager'][$featurepos_pager_id]['total_records']
 
 
 if(count($map_positions) > 0){ ?>
-  <div class="tripal_feature-info-box-desc tripal-info-box-desc">This feature is contained in the following <?php print number_format($total_records) ?> map(s):</div><?php 
+  <div class="tripal_feature-data-block-desc tripal-data-block-desc">This feature is contained in the following <?php print number_format($total_records) ?> map(s):</div><?php 
 
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here

+ 1 - 1
tripal_feature/theme/tripal_feature/tripal_feature_publications.tpl.php

@@ -8,7 +8,7 @@ $feature_pubs = $feature->feature_pub;
 
 
 if (count($feature_pubs) > 0) { ?>
-  <div class="tripal_feature_pub-info-box-desc tripal-info-box-desc"></div> <?php 
+  <div class="tripal_feature_pub-data-block-desc tripal-data-block-desc"></div> <?php 
 
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here

+ 1 - 1
tripal_feature/theme/tripal_feature/tripal_feature_references.tpl.php

@@ -26,7 +26,7 @@ if (count($feature_dbxrefs) > 0 ) {
 
 
 if(count($references) > 0){ ?>
-  <div class="tripal_feature-info-box-desc tripal-info-box-desc">External references for this <?php print $feature->type_id->name ?></div><?php
+  <div class="tripal_feature-data-block-desc tripal-data-block-desc">External references for this <?php print $feature->type_id->name ?></div><?php
    
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here

+ 1 - 1
tripal_feature/theme/tripal_feature/tripal_feature_relationships.tpl.php

@@ -23,7 +23,7 @@ $object_rels = $all_relationships['object'];
 $subject_rels = $all_relationships['subject'];
 
 if (count($object_rels) > 0 or count($subject_rels) > 0) { ?>
-  <div class="tripal_feature-info-box-desc tripal-info-box-desc"></div> <?php
+  <div class="tripal_feature-data-block-desc tripal-data-block-desc"></div> <?php
   
   // first add in the subject relationships.  
   foreach ($subject_rels as $rel_type => $rels){

+ 1 - 1
tripal_feature/theme/tripal_feature/tripal_feature_sequence.tpl.php

@@ -39,7 +39,7 @@ $feature = $variables['node']->feature;
 $featureloc_sequences = $feature->featureloc_sequences;
 
 if ($residues or count($featureloc_sequences) > 0) { ?>
-  <div class="tripal_feature-info-box-desc tripal-info-box-desc"></div> <?php
+  <div class="tripal_feature-data-block-desc tripal-data-block-desc"></div> <?php
   
   // show the alignment sequences first as they are colored with child features
   if(count($featureloc_sequences) > 0){

+ 1 - 1
tripal_feature/theme/tripal_feature/tripal_feature_synonyms.tpl.php

@@ -8,7 +8,7 @@ $feature = tripal_core_expand_chado_vars($feature, 'table', 'feature_synonym', $
 $synonyms = $feature->feature_synonym;
 
 if(count($synonyms) > 0){ ?>
-  <div class="tripal_feature-info-box-desc tripal-info-box-desc">The feature '<?php print $feature->name ?>' has the following synonyms</div><?php
+  <div class="tripal_feature-data-block-desc tripal-data-block-desc">The feature '<?php print $feature->name ?>' has the following synonyms</div><?php
   
   // the $headers array is an array of fields to use as the colum headers. 
   // additional documentation can be found here 

+ 1 - 1
tripal_feature/theme/tripal_feature/tripal_feature_terms.tpl.php

@@ -15,7 +15,7 @@ if ($terms) {
 }
 
 if (count($s_terms) > 0) { ?>
-  <div class="tripal_feature-info-box-desc tripal-info-box-desc">The following terms have been associated with this <?php print $node->feature->type_id->name ?>:</div>  <?php
+  <div class="tripal_feature-data-block-desc tripal-data-block-desc">The following terms have been associated with this <?php print $node->feature->type_id->name ?>:</div>  <?php
   
   // iterate through each term
   $i = 0;

+ 1 - 1
tripal_feature/theme/tripal_organism/tripal_organism_feature_browser.tpl.php

@@ -57,7 +57,7 @@ foreach ($results as $result) {
 // only show this block if it is enabled
 if ($enabled) { 
   if (count($features) > 0) { ?>
-    <div class="tripal_organism-info-box-desc tripal-info-box-desc">The following browser provides a quick view for new visitors.  Use the searching mechanism to find specific features.</div> <?php
+    <div class="tripal_organism-data-block-desc tripal-data-block-desc">The following browser provides a quick view for new visitors.  Use the searching mechanism to find specific features.</div> <?php
     
     // the $headers array is an array of fields to use as the colum headers.
     // additional documentation can be found here

+ 2 - 2
tripal_feature/theme/tripal_organism/tripal_organism_feature_counts.tpl.php

@@ -13,7 +13,7 @@ if(property_exists($organism, 'feature_counts')) {
 // only show this block if it is enabled
 if ($enabled) { 
   if (count($types) > 0){ ?>
-    <div class="tripal_organism-info-box-desc tripal-info-box-desc">The following data types are currently present for this organism</div> <?php
+    <div class="tripal_organism-data-block-desc tripal-data-block-desc">The following data types are currently present for this organism</div> <?php
     // let admins know they can customize the terms that appear in the list
     print theme('tripal_admin_message', array('message' => "
       Administrators, you can customize the types of terms that appear in this report by 
@@ -48,7 +48,7 @@ if ($enabled) {
    } 
    else { 
     if (user_access('access administration pages')) { ?>
-      <div class="tripal_organism-info-box-desc tripal-info-box-desc">The following data types are currently present for this organism</div> <?php 
+      <div class="tripal_organism-data-block-desc tripal-data-block-desc">The following data types are currently present for this organism</div> <?php 
       print theme('tripal_admin_message', array('message' => "
          Administrators, to view the feature type report:
          <ul>

+ 5 - 4
tripal_feature/tripal_feature.info

@@ -1,12 +1,13 @@
 name = Tripal Feature
-description = A module for interfacing the GMOD chado database with Drupal, providing viewing, inserting and editing of chado features.
+description = Supports the sequence (feature) tables of Chado by providing pages for importing, viewing and editing of sequences (features). Table list at: http://gmod.org/wiki/Chado_Sequence_Module.
 core = 7.x
 project = tripal_feature
 package = Tripal
-version = 7.x-2.0-beta1
+version = 7.x-2.0a
+
+stylesheets[all][] = theme/css/tripal_feature.css
+scripts[]          = theme/js/tripal_feature.js
 
-dependencies[] = search
-dependencies[] = path
 dependencies[] = tripal_core
 dependencies[] = tripal_views
 dependencies[] = tripal_db

+ 1 - 2
tripal_feature/tripal_feature.module

@@ -25,8 +25,7 @@ require_once "includes/tripal_feature.blocks.inc";
  * @ingroup tripal_feature
  */
 function tripal_feature_init() {
-  drupal_add_css(drupal_get_path('module', 'tripal_feature') . '/theme/css/tripal_feature.css');
-  drupal_add_js(drupal_get_path('module', 'tripal_feature') . '/theme/js/tripal_feature.js');
+
 }
 
 /**

+ 0 - 7
tripal_featuremap/theme/css/tripal_featuremap.css

@@ -1,7 +0,0 @@
-#tripal-featuremap-edit-properties-table {
-  width: auto;
-}
-
-#tripal-featuremap-edit-properties-table .form-item {
-  white-space: normal;
-}

+ 0 - 0
tripal_featuremap/theme/js/tripal_featuremap.js


+ 1 - 1
tripal_featuremap/theme/tripal_featuremap/tripal_featuremap.base.tpl.php → tripal_featuremap/theme/tripal_featuremap/tripal_featuremap_base.tpl.php

@@ -5,7 +5,7 @@ $featuremap  = $variables['node']->featuremap;
 // expand the description field
 $featuremap = tripal_core_expand_chado_vars($featuremap, 'field', 'featuremap.description'); ?>
 
-<div class="tripal_featuremap-info-box-desc tripal-info-box-desc"></div> <?php 
+<div class="tripal_featuremap-data-block-desc tripal-data-block-desc"></div> <?php 
 
 // the $headers array is an array of fields to use as the colum headers. 
 // additional documentation can be found here 

+ 1 - 1
tripal_featuremap/theme/tripal_featuremap/tripal_featuremap.featurepos.tpl.php → tripal_featuremap/theme/tripal_featuremap/tripal_featuremap_featurepos.tpl.php

@@ -38,7 +38,7 @@ $total_features = $_SESSION['chado_pager'][$featurepos_pager_id]['total_records'
 
 
 if(count($feature_positions) > 0){ ?>
-  <div class="tripal_featuremap-info-box-desc tripal-info-box-desc">This map contains <?php print number_format($total_features) ?> features:</div> <?php 
+  <div class="tripal_featuremap-data-block-desc tripal-data-block-desc">This map contains <?php print number_format($total_features) ?> features:</div> <?php 
   
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here

+ 0 - 0
tripal_featuremap/theme/tripal_featuremap/tripal_featuremap.properties.tpl.php → tripal_featuremap/theme/tripal_featuremap/tripal_featuremap_properties.tpl.php


+ 1 - 1
tripal_featuremap/theme/tripal_featuremap/tripal_featuremap.publication.tpl.php → tripal_featuremap/theme/tripal_featuremap/tripal_featuremap_publication.tpl.php

@@ -8,7 +8,7 @@ $featuremap_pubs = $featuremap->featuremap_pub;
 
 
 if (count($featuremap_pubs) > 0) { ?>
-  <div class="tripal_featuremap_pub-info-box-desc tripal-info-box-desc"></div> <?php 
+  <div class="tripal_featuremap_pub-data-block-desc tripal-data-block-desc"></div> <?php 
 
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here

+ 1 - 1
tripal_featuremap/theme/tripal_featuremap/tripal_featuremap.references.tpl.php → tripal_featuremap/theme/tripal_featuremap/tripal_featuremap_references.tpl.php

@@ -14,7 +14,7 @@ if (count($featuremap_dbxrefs) > 0 ) {
 
 
 if(count($references) > 0){ ?>
-  <div class="tripal_featuremap-info-box-desc tripal-info-box-desc">External references for this map</div><?php
+  <div class="tripal_featuremap-data-block-desc tripal-data-block-desc">External references for this map</div><?php
    
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here

+ 0 - 0
tripal_featuremap/theme/tripal_featuremap/tripal_featuremap.teaser.tpl.php → tripal_featuremap/theme/tripal_featuremap/tripal_featuremap_teaser.tpl.php


+ 0 - 0
tripal_featuremap/theme/tripal_featuremap.help.tpl.php → tripal_featuremap/theme/tripal_featuremap_help.tpl.php


+ 2 - 4
tripal_featuremap/tripal_featuremap.info

@@ -1,15 +1,13 @@
 name = Tripal Feature Map
-description = A module for interfacing the GMOD chado database with Drupal, providing viewing, inserting and editing of maps (e.g. genetic maps).
+description = Supports the map tables of Chado by providing pages for viewing and editing of maps. Table list at: http://gmod.org/wiki/Chado_Map_Module
 core = 7.x
 project = tripal_featuremap
 package = Tripal
-version = 7.x-2.0-beta1
+version = 7.x-2.0a
 
 dependencies[] = tripal_core
 dependencies[] = tripal_views
 dependencies[] = tripal_organism
 dependencies[] = tripal_feature
-dependencies[] = search
-dependencies[] = path
 dependencies[] = tripal_cv
 

+ 8 - 9
tripal_featuremap/tripal_featuremap.module

@@ -18,8 +18,7 @@ require('includes/tripal_featuremap.chado_node.inc');
  * @ingroup tripal_featuremap
  */
 function tripal_featuremap_init() {
-  drupal_add_css(drupal_get_path('module', 'tripal_featuremap') . '/theme/css/tripal_featuremap.css');
-  drupal_add_js(drupal_get_path('module', 'tripal_featuremap') . '/theme/js/tripal_featuremap.js');
+
 }
 
 
@@ -179,36 +178,36 @@ function tripal_featuremap_theme($existing, $type, $theme, $path) {
     ),
     'tripal_featuremap_base' => array(
       'variables' => array('node' => NULL),
-      'template' => 'tripal_featuremap.base',
+      'template' => 'tripal_featuremap_base',
       'path' => "$path/theme/tripal_featuremap",
     ),
     'tripal_featuremap_properties' => array(
       'variables' => array('node' => NULL),
-      'template' => 'tripal_featuremap.properties',
+      'template' => 'tripal_featuremap_properties',
       'path' => "$path/theme/tripal_featuremap",
     ),
     'tripal_featuremap_featurepos' => array(
       'variables' => array('node' => NULL),
-      'template' => 'tripal_featuremap.featurepos',
+      'template' => 'tripal_featuremap_featurepos',
       'path' => "$path/theme/tripal_featuremap",
     ),
     'tripal_featuremap_publication' => array(
       'variables' => array('node' => NULL),
-      'template' => 'tripal_featuremap.publication',
+      'template' => 'tripal_featuremap_publication',
       'path' => "$path/theme/tripal_featuremap",
     ),
     'tripal_featuremap_references' => array(
       'variables' => array('node' => NULL),
-      'template' => 'tripal_featuremap.references',
+      'template' => 'tripal_featuremap_references',
       'path' => "$path/theme/tripal_featuremap",
     ),
     'tripal_featuremap_help' => array(
-      'template' => 'tripal_featuremap.help',
+      'template' => 'tripal_featuremap_help',
       'variables' =>  array(NULL),
       'path' => "$path/theme",
     ),
     'tripal_featuremap_teaser' => array(
-      'template' => 'tripal_featuremap.teaser',
+      'template' => 'tripal_featuremap_teaser',
       'variables' =>  array(NULL),
       'path' => "$path/theme/tripal_featuremap",
     ),

+ 0 - 0
tripal_genetic/theme/css/tripal_genetic.css


+ 0 - 0
tripal_genetic/theme/js/tripal_genetic.js


+ 1 - 1
tripal_genetic/theme/tripal_feature/tripal_feature.genotypes.tpl.php → tripal_genetic/theme/tripal_feature/tripal_feature_genotypes.tpl.php

@@ -44,7 +44,7 @@ $total_records = $_SESSION['chado_pager'][$feature_pager_id]['total_records'];
 
 // now iterate through the feature genotypes and print a paged table.
 if (count($feature_genotypes) > 0) {?>
-  <div class="tripal_feature-info-box-desc tripal-info-box-desc">This following <?php print number_format($total_records) ?> genotype(s) have been recorded for this feature.</div><?php 
+  <div class="tripal_feature-data-block-desc tripal-data-block-desc">This following <?php print number_format($total_records) ?> genotype(s) have been recorded for this feature.</div><?php 
   
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here

+ 0 - 0
tripal_genetic/theme/tripal_genetic.help.tpl.php


+ 0 - 0
tripal_analysis/theme/js/tripal_analysis.js → tripal_genetic/theme/tripal_genetic_help.tpl.php


+ 1 - 1
tripal_genetic/theme/tripal_stock/tripal_stock.genotypes.tpl.php → tripal_genetic/theme/tripal_stock/tripal_stock_genotypes.tpl.php

@@ -34,7 +34,7 @@ $total_records = $_SESSION['chado_pager'][$stock_pager_id]['total_records'];
 
 // now iterate through the stock genotypes and print a paged table.
 if (count($stock_genotypes) > 0) {?>
-  <div class="tripal_stock-info-box-desc tripal-info-box-desc">The following <?php print number_format($total_records) ?> genotype(s) have been recorded for this stock.</div> <?php
+  <div class="tripal_stock-data-block-desc tripal-data-block-desc">The following <?php print number_format($total_records) ?> genotype(s) have been recorded for this stock.</div> <?php
   
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here

+ 2 - 2
tripal_genetic/tripal_genetic.info

@@ -1,9 +1,9 @@
 name = Tripal Genetic
-description = A module for interfacing the GMOD chado database with Drupal, providing viewing of genetic data
+description = Supports the genetic tables of Chado by providing pages for viewing of genetic data associated with stocks and features. Table list at: http://gmod.org/wiki/Chado_Genetic_Module
 core = 7.x
 project = tripal_genetic
 package = Tripal
-version = 7.x-2.0-beta1
+version = 7.x-2.0a
 
 dependencies[] = tripal_core
 dependencies[] = tripal_views

+ 3 - 3
tripal_genetic/tripal_genetic.module

@@ -91,16 +91,16 @@ function tripal_genetic_theme($existing, $type, $theme, $path) {
   $items = array(
     'tripal_feature_genotypes' => array(
       'variables' => array('node' => NULL),
-      'template' => 'tripal_feature.genotypes',
+      'template' => 'tripal_feature_genotypes',
       'path' => "$path/theme/tripal_feature",
     ),
     'tripal_stock_genotypes' => array(
       'variables' => array('node' => NULL),
-      'template' => 'tripal_stock.genotypes',
+      'template' => 'tripal_stock_genotypes',
       'path' => "$path/theme/tripal_stock",
     ),
     'tripal_genetic_help' => array(
-      'template' => 'tripal_genetic.help',
+      'template' => 'tripal_genetic_help',
       'variables' =>  array(NULL),
       'path' => "$path/theme/",
     ),

+ 0 - 0
tripal_library/theme/css/tripal_library.css


+ 0 - 0
tripal_library/theme/js/tripal_library.js


+ 1 - 1
tripal_library/theme/tripal_feature/tripal_feature.libraries.tpl.php → tripal_library/theme/tripal_feature/tripal_feature_libraries.tpl.php

@@ -9,7 +9,7 @@ $library_features = $feature->library_feature;
 
 
 if (count($library_features) > 0) {?>
-  <div class="tripal_feature-info-box-desc tripal-info-box-desc">The following libraries are associated with this feature.</div> <?php 
+  <div class="tripal_feature-data-block-desc tripal-data-block-desc">The following libraries are associated with this feature.</div> <?php 
   
   // the $headers array is an array of fields to use as the colum headers. 
   // additional documentation can be found here 

+ 1 - 1
tripal_library/theme/tripal_library/tripal_library.base.tpl.php → tripal_library/theme/tripal_library/tripal_library_base.tpl.php

@@ -6,7 +6,7 @@ $library  = $variables['node']->library;
 $libprop = tripal_library_get_property($library->library_id, 'Library Description');
 $description = $libprop->value; ?>
 
-<div class="tripal_library-info-box-desc tripal-info-box-desc"></div> <?php 
+<div class="tripal_library-data-block-desc tripal-data-block-desc"></div> <?php 
 
 // the $headers array is an array of fields to use as the colum headers. 
 // additional documentation can be found here 

+ 0 - 0
tripal_library/theme/tripal_library/tripal_library.properties.tpl.php → tripal_library/theme/tripal_library/tripal_library_properties.tpl.php


+ 1 - 1
tripal_library/theme/tripal_library/tripal_library.publications.tpl.php → tripal_library/theme/tripal_library/tripal_library_publications.tpl.php

@@ -8,7 +8,7 @@ $library_pubs = $library->library_pub;
 
 
 if (count($library_pubs) > 0) { ?>
-  <div class="tripal_library_pub-info-box-desc tripal-info-box-desc"></div> <?php 
+  <div class="tripal_library_pub-data-block-desc tripal-data-block-desc"></div> <?php 
 
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here

+ 1 - 1
tripal_library/theme/tripal_library/tripal_library.references.tpl.php → tripal_library/theme/tripal_library/tripal_library_references.tpl.php

@@ -14,7 +14,7 @@ if (count($library_dbxrefs) > 0 ) {
 
 
 if(count($references) > 0){ ?>
-  <div class="tripal_library-info-box-desc tripal-info-box-desc">External references for this <?php print $library->type_id->name ?></div><?php
+  <div class="tripal_library-data-block-desc tripal-data-block-desc">External references for this <?php print $library->type_id->name ?></div><?php
    
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here

+ 1 - 1
tripal_library/theme/tripal_library/tripal_library.synonyms.tpl.php → tripal_library/theme/tripal_library/tripal_library_synonyms.tpl.php

@@ -8,7 +8,7 @@ $library = tripal_core_expand_chado_vars($library, 'table', 'library_synonym', $
 $synonyms = $library->library_synonym;
 
 if(count($synonyms) > 0){ ?>
-  <div class="tripal_library-info-box-desc tripal-info-box-desc">The library '<?php print $library->name ?>' has the following synonyms</div><?php
+  <div class="tripal_library-data-block-desc tripal-data-block-desc">The library '<?php print $library->name ?>' has the following synonyms</div><?php
   
   // the $headers array is an array of fields to use as the colum headers. 
   // additional documentation can be found here 

+ 0 - 0
tripal_library/theme/tripal_library/tripal_library.teaser.tpl.php → tripal_library/theme/tripal_library/tripal_library_teaser.tpl.php


+ 1 - 1
tripal_library/theme/tripal_library/tripal_library.terms.tpl.php → tripal_library/theme/tripal_library/tripal_library_terms.tpl.php

@@ -13,7 +13,7 @@ foreach ($terms as $term) {
 }
 
 if (count($s_terms) > 0) { ?>
-  <div class="tripal_library-info-box-desc tripal-info-box-desc">The following terms have been associated with this <?php print $node->library->type_id->name ?>:</div>  <?php
+  <div class="tripal_library-data-block-desc tripal-data-block-desc">The following terms have been associated with this <?php print $node->library->type_id->name ?>:</div>  <?php
   
   // iterate through each term
   $i = 0;

+ 0 - 0
tripal_library/theme/tripal_library.help.tpl.php → tripal_library/theme/tripal_library_help.tpl.php


+ 1 - 1
tripal_library/theme/tripal_organism/tripal_organism.libraries.tpl.php → tripal_library/theme/tripal_organism/tripal_organism_libraries.tpl.php

@@ -9,7 +9,7 @@ $libraries = $organism->library;
 
 
 if (count($libraries) > 0) {?>
-  <div class="tripal_organism-info-box-desc tripal-info-box-desc">The following libraries are associated with this organism.</div> <?php 
+  <div class="tripal_organism-data-block-desc tripal-data-block-desc">The following libraries are associated with this organism.</div> <?php 
   
   // the $headers array is an array of fields to use as the colum headers. 
   // additional documentation can be found here 

+ 2 - 4
tripal_library/tripal_library.info

@@ -1,12 +1,10 @@
 name = Tripal Library
-description = A module for interfacing the GMOD chado database with Drupal, providing viewing, inserting and editing of lbraries.
+description = Supports the library tables of Chado by providing pages for viewing and editing of biological libraries. Table list at: http://gmod.org/wiki/Chado_Library_Module
 core = 7.x
 project = tripal_library
 package = Tripal
-version = 7.x-2.0-beta1
+version = 7.x-2.0a
 
-dependencies[] = search
-dependencies[] = path
 dependencies[] = tripal_core
 dependencies[] = tripal_views
 dependencies[] = tripal_organism

+ 10 - 10
tripal_library/tripal_library.module

@@ -142,36 +142,36 @@ function tripal_library_theme($existing, $type, $theme, $path) {
     // tripal_library templates
     'tripal_library_base' => array(
       'variables' => array('node' => NULL),
-      'template' => 'tripal_library.base',
+      'template' => 'tripal_library_base',
       'path' => "$path/theme/tripal_library",
     ),
     'tripal_library_properties' => array(
       'variables' => array('node' => NULL),
-      'template' => 'tripal_library.properties',
+      'template' => 'tripal_library_properties',
       'path' => "$path/theme/tripal_library",
     ),
     'tripal_library_publications' => array(
       'variables' => array('node' => NULL),
-      'template' => 'tripal_library.publications',
+      'template' => 'tripal_library_publications',
       'path' => "$path/theme/tripal_library",
     ),
     'tripal_library_references' => array(
       'variables' => array('node' => NULL),
-      'template' => 'tripal_library.references',
+      'template' => 'tripal_library_references',
       'path' => "$path/theme/tripal_library",
     ),
     'tripal_library_synonyms' => array(
       'variables' => array('node' => NULL),
-      'template' => 'tripal_library.synonyms',
+      'template' => 'tripal_library_synonyms',
       'path' => "$path/theme/tripal_library",
     ),
     'tripal_library_terms' => array(
       'variables' => array('node' => NULL),
-      'template' => 'tripal_library.terms',
+      'template' => 'tripal_library_terms',
       'path' => "$path/theme/tripal_library",
     ),
     'tripal_library_help' => array(
-      'template' => 'tripal_library.help',
+      'template' => 'tripal_library_help',
       'variables' =>  array(NULL),
       'path' => "$path/theme",
     ),
@@ -179,21 +179,21 @@ function tripal_library_theme($existing, $type, $theme, $path) {
     // teaser
     'tripal_library_teaser' => array(
       'variables' => array('node' => NULL),
-      'template' => 'tripal_library.teaser',
+      'template' => 'tripal_library_teaser',
       'path' => "$path/theme/tripal_library",
     ),
 
     // tripal_organism templates
     'tripal_organism_libraries' => array(
       'variables' => array('node' => NULL),
-      'template' => 'tripal_organism.libraries',
+      'template' => 'tripal_organism_libraries',
       'path' => "$path/theme/tripal_organism",
     ),
 
     // tripal_feature templates
     'tripal_feature_libraries' => array(
       'variables' => array('node' => NULL),
-      'template' => 'tripal_feature.libraries',
+      'template' => 'tripal_feature_libraries',
       'path' => "$path/theme/tripal_feature",
     ),
 

+ 0 - 0
tripal_natural_diversity/theme/css/tripal_natural_diversity.css


+ 0 - 0
tripal_natural_diversity/theme/js/tripal_natural_diversity.js


+ 1 - 1
tripal_natural_diversity/theme/tripal_feature/tripal_feature.nd_genotypes.tpl.php → tripal_natural_diversity/theme/tripal_feature/tripal_feature_nd_genotypes.tpl.php

@@ -67,7 +67,7 @@ $total_records = $_SESSION['chado_pager'][$feature_pager_id]['total_records'];
 
 // now iterate through the feature genotypes and print a paged table.
 if (count($feature_genotypes) > 0) { ?>
-  <div class="tripal_feature-info-box-desc tripal-info-box-desc">This following <?php print number_format($total_records) ?> genotype(s) have been recorded for this feature.</div> <?php 
+  <div class="tripal_feature-data-block-desc tripal-data-block-desc">This following <?php print number_format($total_records) ?> genotype(s) have been recorded for this feature.</div> <?php 
 
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here

+ 0 - 0
tripal_natural_diversity/theme/tripal_natural_diversity.help.tpl.php → tripal_natural_diversity/theme/tripal_natural_diversity_help.tpl.php


+ 1 - 1
tripal_natural_diversity/theme/tripal_stock/tripal_stock.nd_genotypes.tpl.php → tripal_natural_diversity/theme/tripal_stock/tripal_stock_nd_genotypes.tpl.php

@@ -102,7 +102,7 @@ $total_records = $_SESSION['chado_pager'][$stock_pager_id]['total_records'];
 
 // now iterate through the feature genotypes and print a paged table.
 if (count($genotypes) > 0) { ?>
-  <div class="tripal_feature-info-box-desc tripal-info-box-desc">The following <?php print number_format($total_records) ?> genotype(s) have been recorded for this feature.</div> <?php 
+  <div class="tripal_feature-data-block-desc tripal-data-block-desc">The following <?php print number_format($total_records) ?> genotype(s) have been recorded for this feature.</div> <?php 
 
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here

+ 1 - 1
tripal_natural_diversity/theme/tripal_stock/tripal_stock.nd_phenotypes.tpl.php → tripal_natural_diversity/theme/tripal_stock/tripal_stock_nd_phenotypes.tpl.php

@@ -66,7 +66,7 @@ if (count($nd_experiment_stocks) > 0) {
 }
 
 if (count($phenotypes) > 0) {?>
-  <div class="tripal_stock-info-box-desc tripal-info-box-desc">This following phenotypes have been recorded for this stock.</div><?php 
+  <div class="tripal_stock-data-block-desc tripal-data-block-desc">This following phenotypes have been recorded for this stock.</div><?php 
 
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here

+ 2 - 2
tripal_natural_diversity/tripal_natural_diversity.info

@@ -1,9 +1,9 @@
 name = Tripal Natural Diversity
-description = A module for interfacing the GMOD chado database with Drupal, providing viewing of Natural Diversity data
+description = Supports the natural diversity (ND) tables of Chado by providing pages for viewing of data in the ND tables as associated with features, stocks and projects. Table list at: http://gmod.org/wiki/Chado_Natural_Diversity_Module
 core = 7.x
 project = tripal_natural_diversity
 package = Tripal
-version = 7.x-2.0-beta1
+version = 7.x-2.0a
 
 dependencies[] = tripal_core
 dependencies[] = tripal_views

+ 4 - 4
tripal_natural_diversity/tripal_natural_diversity.module

@@ -92,22 +92,22 @@ function tripal_natural_diversity_theme($existing, $type, $theme, $path) {
     // tripal_feature templates
     'tripal_feature_nd_genotypes' => array(
       'variables' => array('node' => NULL),
-      'template' => 'tripal_feature.nd_genotypes',
+      'template' => 'tripal_feature_nd_genotypes',
       'path' => "$path/theme/tripal_feature",
     ),
     // tripal_stock templates
     'tripal_stock_nd_genotypes' => array(
       'variables' => array('node' => NULL),
-      'template' => 'tripal_stock.nd_genotypes',
+      'template' => 'tripal_stock_nd_genotypes',
       'path' => "$path/theme/tripal_stock",
     ),
     'tripal_stock_nd_phenotypes' => array(
       'variables' => array('node' => NULL),
-      'template' => 'tripal_stock.nd_phenotypes',
+      'template' => 'tripal_stock_nd_phenotypes',
       'path' => "$path/theme/tripal_stock",
     ),
     'tripal_natural_diversity_help' => array(
-      'template' => 'tripal_natural_diversity.help',
+      'template' => 'tripal_natural_diversity_help',
       'variables' =>  array(NULL),
       'path' => "$path/theme",
     ),

+ 0 - 4
tripal_organism/theme/css/tripal_organism.css

@@ -1,4 +0,0 @@
-#tripal_organism-base-box img {
-  float: left;
-  margin: 0px 10px 0px 0px;
-}

+ 0 - 0
tripal_organism/theme/js/tripal_organism.js


+ 1 - 1
tripal_organism/theme/tripal_organism/tripal_organism_base.tpl.php

@@ -3,7 +3,7 @@
 $organism  = $variables['node']->organism;
 $organism = tripal_core_expand_chado_vars($organism,'field','organism.comment'); ?>
 
-<div class="tripal_organism-info-box-desc tripal-info-box-desc"></div><?php
+<div class="tripal_organism-data-block-desc tripal-data-block-desc"></div><?php
 
 // generate the image tag
 $image = '';

+ 1 - 1
tripal_organism/theme/tripal_organism/tripal_organism_references.tpl.php

@@ -20,7 +20,7 @@ if (count($organism_dbxrefs) > 0 ) {
 
 
 if(count($references) > 0){ ?>
-  <div class="tripal_organism-info-box-desc tripal-info-box-desc">External references for this organism</div><?php
+  <div class="tripal_organism-data-block-desc tripal-data-block-desc">External references for this organism</div><?php
    
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here

+ 2 - 4
tripal_organism/tripal_organism.info

@@ -1,12 +1,10 @@
 name = Tripal Organism
-description = A module for interfacing organisms from the GMOD chado database with Drupal. It provides viewing, inserting and editing of organisms.
+description = Supports the organism tables of Chado by providing pages for viewing and editing of organisms. Table list at: http://gmod.org/wiki/Chado_Organism_Module
 core = 7.x
 project = tripal_organism
 package = Tripal
-version = 7.x-2.0-beta1
+version = 7.x-2.0a
 configure = admin/tripal/chado/tripal_organism
 
 dependencies[] = tripal_core
 dependencies[] = tripal_views
-dependencies[] = search
-dependencies[] = path

+ 0 - 3
tripal_organism/tripal_organism.module

@@ -18,9 +18,6 @@ require_once "includes/tripal_organism.chado_node.inc";
  */
 function tripal_organism_init() {
 
-  // add the jGCharts JS and CSS
-  drupal_add_css(drupal_get_path('module', 'tripal_organism') . '/theme/css/tripal_organism.css');
-  drupal_add_js(drupal_get_path('module', 'tripal_organism') . '/theme/js/tripal_organism.js');
 }
 
 

+ 0 - 0
tripal_phenotype/theme/css/tripal_phenotype.css


+ 0 - 0
tripal_phenotype/theme/js/tripal_phenotype.js


+ 1 - 1
tripal_phenotype/theme/tripal_feature/tripal_feature.phenotypes.tpl.php → tripal_phenotype/theme/tripal_feature/tripal_feature_phenotypes.tpl.php

@@ -17,7 +17,7 @@ $feature_phenotypes = $feature->feature_phenotype;
 
 if(count($feature_phenotypes) > 0){ ?>
   
-  <div class="tripal_feature-info-box-desc tripal-info-box-desc">The feature is associated with the following phenotypes</div><?php
+  <div class="tripal_feature-data-block-desc tripal-data-block-desc">The feature is associated with the following phenotypes</div><?php
 
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here

+ 0 - 0
tripal_phenotype/theme/tripal_phenotype.help.tpl.php → tripal_phenotype/theme/tripal_phenotype_help.tpl.php


+ 2 - 2
tripal_phenotype/tripal_phenotype.info

@@ -1,9 +1,9 @@
 name = Tripal Phenotype
-description = A module for interfacing the GMOD chado database with Drupal providing viewing of phenotype data
+description = Supports the phenotype tables of Chado by providing pages for viewing of phenotype data associated with features. Table list at: http://gmod.org/wiki/Chado_Phenotype_Module
 core = 7.x
 project = tripal_phenotype
 package = Tripal
-version = 7.x-2.0-beta1
+version = 7.x-2.0a
 
 dependencies[] = tripal_core
 dependencies[] = tripal_views

+ 2 - 2
tripal_phenotype/tripal_phenotype.module

@@ -75,11 +75,11 @@ function tripal_phenotype_theme($existing, $type, $theme, $path) {
   $items = array(
     'tripal_feature_phenotypes' => array(
       'variables' => array('node' => NULL),
-      'template' => 'tripal_feature.phenotypes',
+      'template' => 'tripal_feature_phenotypes',
       'path' => "$path/theme/tripal_feature",
     ),
     'tripal_phenotype_help' => array(
-      'template' => 'tripal_phenotype.help',
+      'template' => 'tripal_phenotype_help',
       'variables' =>  array(NULL),
       'path' => "$path/theme",
     ),

+ 0 - 0
tripal_project/theme/css/tripal_project.css


+ 0 - 0
tripal_project/theme/js/tripal_project.js


+ 1 - 1
tripal_project/theme/tripal_project/tripal_project.base.tpl.php → tripal_project/theme/tripal_project/tripal_project_base.tpl.php

@@ -22,7 +22,7 @@ else {
   $description = $projectprop->value;
 } ?>
 
-<div class="tripal_project-info-box-desc tripal-info-box-desc"></div><?php 
+<div class="tripal_project-data-block-desc tripal-data-block-desc"></div><?php 
 
 // the $headers array is an array of fields to use as the colum headers. 
 // additional documentation can be found here 

+ 1 - 1
tripal_project/theme/tripal_project/tripal_project.contact.tpl.php → tripal_project/theme/tripal_project/tripal_project_contact.tpl.php

@@ -7,7 +7,7 @@ $project = tripal_core_expand_chado_vars($project,'table','project_contact', arr
 $project_contacts = $project->project_contact;
 
 if (count($project_contacts) > 0) { ?>
-  <div class="tripal_project-info-box-desc tripal-info-box-desc">The following indivuals or groups have particpated in development or execution of this project</div><?php     
+  <div class="tripal_project-data-block-desc tripal-data-block-desc">The following indivuals or groups have particpated in development or execution of this project</div><?php     
   
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here

+ 1 - 1
tripal_project/theme/tripal_project/tripal_project.properties.tpl.php → tripal_project/theme/tripal_project/tripal_project_properties.tpl.php

@@ -20,7 +20,7 @@ if ($projectprops) {
 
 
 if (count($properties) > 0) { ?>
-  <div class="tripal_project-info-box-desc tripal-info-box-desc">Additional information about this project:</div><?php
+  <div class="tripal_project-data-block-desc tripal-data-block-desc">Additional information about this project:</div><?php
   
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here

+ 1 - 1
tripal_project/theme/tripal_project/tripal_project.publications.tpl.php → tripal_project/theme/tripal_project/tripal_project_publications.tpl.php

@@ -8,7 +8,7 @@ $project_pubs = $project->project_pub;
 
 
 if (count($project_pubs) > 0) { ?>
-  <div class="tripal_project_pub-info-box-desc tripal-info-box-desc"></div> <?php 
+  <div class="tripal_project_pub-data-block-desc tripal-data-block-desc"></div> <?php 
 
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here

+ 1 - 1
tripal_project/theme/tripal_project/tripal_project.relationships.tpl.php → tripal_project/theme/tripal_project/tripal_project_relationships.tpl.php

@@ -23,7 +23,7 @@ $object_rels = $all_relationships['object'];
 $subject_rels = $all_relationships['subject'];
 
 if (count($object_rels) > 0 or count($subject_rels) > 0) { ?>
-  <div class="tripal_project-info-box-desc tripal-info-box-desc">This project is related to the following other projects:</div> <?php
+  <div class="tripal_project-data-block-desc tripal-data-block-desc">This project is related to the following other projects:</div> <?php
 
   // the $headers array is an array of fields to use as the colum headers.
   // additional documentation can be found here

+ 0 - 0
tripal_project/theme/tripal_project/tripal_project.teaser.tpl.php → tripal_project/theme/tripal_project/tripal_project_teaser.tpl.php


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