Cleaned up all old CSS and JS (except CV modulee), added CSS and JS to .info file where needed, and updated the module descriptions in the .info fiels

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;
-}

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

tripal_analysis/tripal_analysis.module

@@ -21,8 +21,7 @@ require_once "api/tripal_analysis.schema.api.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');
+
 }
 
 

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

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;
-}

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

tripal_contact/tripal_contact.module

@@ -37,8 +37,6 @@ 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');
 
 }
 

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

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"]) {

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

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

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');
 }
 /**
  *

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

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

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');
+
 }
 
 /**

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;
-}

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
 

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');
+
 }
 
 

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

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

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

tripal_organism/theme/css/tripal_organism.css

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

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

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');
 }
 
 

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

tripal_project/tripal_project.info

@@ -1,9 +1,9 @@
 name = Tripal Project
-description = A module for interfacing the GMOD chado database with Drupal, providing viewing of projects
+description = Supports the project tables of Chado by providing pages for viewing and editing of projects. Table list at: http://gmod.org/wiki/Chado_General_Module
 core = 7.x
 project = tripal_project
 package = Tripal
-version = 7.x-2.0-beta1
+version = 7.x-2.0a
 configure = admin/tripal/chado/tripal_project
 
 dependencies[] = tripal_core

tripal_pub/theme/css/tripal_pub.css

@@ -1,19 +1,3 @@
-#tripal-pub-edit-properties-table {
-  width: auto;
-}
-
-#tripal-pub-edit-properties-table .form-item {
-  white-space: normal;
-}
-
-.tripal_pub-obsolete {
-   color: red;
-   font-weight: bold;
-   font-style: italic;
-   padding-bottom: 15px; 
-   text-align: center;
-}
-
 /*
  * Importer Form Table 
  */

tripal_pub/tripal_pub.info

@@ -1,9 +1,11 @@
 name = Tripal Publication
-description = A module for interfacing the GMOD chado database with Drupal, providing viewing of publications
+description = Supports the pub (publication) tables of Chado by providing pages for importing, viewing, and editing of publications. Table list at: http://gmod.org/wiki/Chado_Publication_Module
 core = 7.x
 project = tripal_pub
 package = Tripal
-version = 7.x-2.0-beta1
+version = 7.x-2.0a
+
+stylesheets[all][] = theme/css/tripal_pub.css
 
 dependencies[] = tripal_core
 dependencies[] = tripal_views

tripal_pub/tripal_pub.module

@@ -27,8 +27,7 @@ require_once "includes/importers/tripal_pub.AGL.inc";
  * @ingroup tripal_pub
  */
 function tripal_pub_init() {
-  drupal_add_css(drupal_get_path('module', 'tripal_pub') . '/theme/css/tripal_pub.css');
-  drupal_add_js(drupal_get_path('module', 'tripal_pub') . '/theme/js/tripal_pub.js');
+
 }
 
 /**

tripal_stock/tripal_stock.info

@@ -1,9 +1,9 @@
 name = Tripal Stock
-description = A module for interfacing the GMOD chado database with Drupal, providing viewing, inserting and editing of stocks (including stock relationships and properties).
+description = Supports the stock tables of Chado by providing pages for viewing, and editing of stocks. Table list: http://gmod.org/wiki/Chado_Stock_Module
 core = 7.x
 project = tripal_stock
 package = Tripal
-version = 7.x-2.0-beta1
+version = 7.x-2.0a
 
 dependencies[] = tripal_core
 dependencies[] = tripal_views

tripal_views/tripal_views.info

@@ -1,9 +1,9 @@
 name = Tripal Views
-description = This module provides integration with Drupal Views. Other Tripal modules may have an optional dependency with this module and once enabled Views support becomes active for those modules.  This module provides a way to integrate Materialized Views and Chado Tables with Views. It also integrates the Views Data Export module to allow for downloads of Views into Excel, CSV and FASTA formats.
+description = Integrates all Chado tables with Drupal Views and provides basic searching for administrators and site visitors and provides a range of flexibility for creating custom pages without the need for programming.
 core = 7.x
 project = tripal_core
 package = Tripal
-version = 7.x-2.0-beta1
+version = 7.x-2.0a
 configure = admin/tripal/views-integration
 
 files[] = views/handlers/tripal_views_handler_filter_textarea.inc

tripal_views/tripal_views.views.inc

@@ -124,7 +124,7 @@ function tripal_views_views_pre_render(&$view) {
 
   // Add css if tripal admin tagged view
   if ($view->tag == 'tripal admin') {
-    $tripal_admin_view_css = drupal_get_path('module', 'tripal_views') . '/theme/tripal_views_admin_views.css';
+    $tripal_admin_view_css = drupal_get_path('module', 'tripal_views') . '/theme/css/tripal_views_admin_views.css';
     drupal_add_css($tripal_admin_view_css);
   }