Diff
Modified: branches/biocat/Rakefile (2367 => 2368)
--- branches/biocat/Rakefile 2010-03-31 12:50:51 UTC (rev 2367)
+++ branches/biocat/Rakefile 2010-03-31 13:15:32 UTC (rev 2368)
@@ -22,6 +22,11 @@
desc 'Refresh workflow metadata'
task "myexp:refresh:workflows" do
require File.dirname(__FILE__) + '/config/environment'
+
+ conn = ActiveRecord::Base.connection
+
+ conn.execute('TRUNCATE workflow_processors')
+
Workflow.find(:all).each do |w|
w.extract_metadata
end
@@ -30,6 +35,18 @@
desc 'Import data from BioCatalogue'
task "myexp:import:biocat" do
require File.dirname(__FILE__) + '/config/environment'
+
+ Contribution.delete_all("contributable_type = 'Service'")
+
+ conn = ActiveRecord::Base.connection
+
+ conn.execute('TRUNCATE service_categories')
+ conn.execute('TRUNCATE service_deployments')
+ conn.execute('TRUNCATE service_providers')
+ conn.execute('TRUNCATE service_tags')
+ conn.execute('TRUNCATE service_types')
+ conn.execute('TRUNCATE services')
+
BioCatalogueImport.import_biocatalogue
end
Modified: branches/biocat/app/controllers/services_controller.rb (2367 => 2368)
--- branches/biocat/app/controllers/services_controller.rb 2010-03-31 12:50:51 UTC (rev 2367)
+++ branches/biocat/app/controllers/services_controller.rb 2010-03-31 13:15:32 UTC (rev 2368)
@@ -42,7 +42,7 @@
protected
def find_services
- @contributables = BioCatService.find(:all,
+ @contributables = Service.find(:all,
:order => "created_at DESC",
:page => { :size => 20,
:current => params[:page] })
@@ -50,7 +50,7 @@
def find_service
begin
- service = BioCatService.find(params[:id])
+ service = Service.find(params[:id])
@contributable = service
@@ -71,7 +71,7 @@
def error(notice, message, attr=:id)
flash[:error] = notice
- (err = BioCatService.new.errors).add(attr, message)
+ (err = Service.new.errors).add(attr, message)
respond_to do |format|
format.html { redirect_to services_url }
Deleted: branches/biocat/app/models/bio_cat_service.rb (2367 => 2368)
--- branches/biocat/app/models/bio_cat_service.rb 2010-03-31 12:50:51 UTC (rev 2367)
+++ branches/biocat/app/models/bio_cat_service.rb 2010-03-31 13:15:32 UTC (rev 2368)
@@ -1,14 +0,0 @@
-# myExperiment: app/models/bio_cat_service.rb
-#
-# Copyright (c) 2007 University of Manchester and the University of Southampton.
-# See license.txt for details.
-
-require 'lib/acts_as_site_entity'
-require 'lib/acts_as_contributable'
-
-class BioCatService < ActiveRecord::Base
- acts_as_site_entity
- acts_as_contributable
- acts_as_structured_data
-end
-
Copied: branches/biocat/app/models/service.rb (from rev 2363, branches/biocat/app/models/bio_cat_service.rb) (0 => 2368)
--- branches/biocat/app/models/service.rb (rev 0)
+++ branches/biocat/app/models/service.rb 2010-03-31 13:15:32 UTC (rev 2368)
@@ -0,0 +1,14 @@
+# myExperiment: app/models/service.rb
+#
+# Copyright (c) 2007 University of Manchester and the University of Southampton.
+# See license.txt for details.
+
+require 'lib/acts_as_site_entity'
+require 'lib/acts_as_contributable'
+
+class Service < ActiveRecord::Base
+ acts_as_site_entity
+ acts_as_contributable
+ acts_as_structured_data
+end
+
Deleted: branches/biocat/app/views/services/_table.rhtml (2367 => 2368)
--- branches/biocat/app/views/services/_table.rhtml 2010-03-31 12:50:51 UTC (rev 2367)
+++ branches/biocat/app/views/services/_table.rhtml 2010-03-31 13:15:32 UTC (rev 2368)
@@ -1,61 +0,0 @@
-<% query ||= false -%>
-<% odd_row = false -%>
-<% unless collection.empty? %>
-
-<table class="alt_table">
- <% for contributable in collection %>
- <tr class="<%= (odd_row = !odd_row) ? "odd_row" : "even_row" %>">
- <% cache(:controller => 'services_cache', :action ="" 'listing', :id => contributable.id) do -%>
- <td style="width: 100px;">
- <p style="margin-top:0; padding-top:0; text-align: center;"><b>Submitter:</b></p>
- <center><%=h contributable.submitter_label %></center>
- </td>
- <td style="text-align: left;">
-
- <p class="title">
- <%= icon contributable.class.to_s.underscore, nil, nil, nil, '' %>
- <% title = contributable.name %>
- <%= link_to(query ? highlight_all(title, query) : title, service_path(contributable)) %>
- </p>
-
- <p style="font-size: 85%; margin-top: 0; padding-top: 0;">
- <b>Retrieved at:</b> <%= datetime(contributable.created_at, false) %>
- </p>
- <% if false %>
-
- <p style="font-size:85%;"><b>License: </b><%= license_link contributable.license.to_s %></p>
-
- <div class="desc" style="font-size: 85%;">
- <% if contributable.description and contributable.description.length > 0 %>
- <% desc = truncate(strip_html(contributable.description), 500) %>
- <%= query ? highlight_all(desc, query) : desc %>
- <% else -%>
- <span class="none_text">No description</span>
- <% end %>
- </div>
-
- <p style="font-size: 85%;">
- <a href="" algorithm_path(contributable) + '#ratings' -%>"><b>Rating: </b><%= number_with_precision(contributable.rating, 1) %> / 5 (<%= pluralize contributable.ratings_count, 'rating' %>)</a> |
- <a href="" algorithm_path(contributable) + '#comments' -%>"><b>Comments: </b><%= contributable.comments_count %></a> |
- <b>Viewed internally:</b> <%= pluralize Viewing.total_site_viewings_count_for_contribution(contributable.contribution.id), "time" %>
- </p>
-
- <% unless (tags = contributable.tags).empty? %>
- <a href="" algorithm_path(contributable) + '#tags' -%>"><p style="font-size: 85%;"><b>Tags:</b></p></a>
- <div style="display:inline;" class="tags_onesize"><%= tag_cloud_from_collection tags, true %></div>
- <% else %>
- <p style="font-size: 85%;"><i>This Algorithm has no tags!</i></p>
- <% end %>
-<% end %>
- </td>
- <% end %>
-
- <td class="actions" style="width: 80px;">
- <%= icon "show", service_path(contributable), nil, nil, "View" %>
- </td>
- </tr>
- <% end %>
-</table>
-
-<% end %>
-
Copied: branches/biocat/app/views/services/_table.rhtml (from rev 2363, branches/biocat/app/views/bio_cat_services/_table.rhtml) (0 => 2368)
--- branches/biocat/app/views/services/_table.rhtml (rev 0)
+++ branches/biocat/app/views/services/_table.rhtml 2010-03-31 13:15:32 UTC (rev 2368)
@@ -0,0 +1,35 @@
+<% query ||= false -%>
+<% odd_row = false -%>
+<% unless collection.empty? %>
+
+<table class="alt_table">
+ <% for contributable in collection %>
+ <tr class="<%= (odd_row = !odd_row) ? "odd_row" : "even_row" %>">
+ <% cache(:controller => 'services_cache', :action ="" 'listing', :id => contributable.id) do -%>
+ <td style="width: 100px;">
+ <p style="margin-top:0; padding-top:0; text-align: center;"><b>Submitter:</b></p>
+ <center><%= link_to contributable.submitter_label, contributable.submitter_uri %></center>
+ </td>
+ <td style="text-align: left;">
+
+ <p class="title">
+ <%= icon contributable.class.to_s.underscore, nil, nil, nil, '' %>
+ <% title = contributable.name %>
+ <%= link_to(query ? highlight_all(title, query) : title, service_path(contributable)) %>
+ </p>
+
+ <p style="font-size: 85%; margin-top: 0; padding-top: 0;">
+ <b>Retrieved at:</b> <%= datetime(contributable.created_at, false) %>
+ </p>
+ </td>
+ <% end %>
+
+ <td class="actions" style="width: 80px;">
+ <%= icon "show", service_path(contributable), nil, nil, "View" %>
+ </td>
+ </tr>
+ <% end %>
+</table>
+
+<% end %>
+
Modified: branches/biocat/app/views/services/index.rhtml (2367 => 2368)
--- branches/biocat/app/views/services/index.rhtml 2010-03-31 12:50:51 UTC (rev 2367)
+++ branches/biocat/app/views/services/index.rhtml 2010-03-31 13:15:32 UTC (rev 2368)
@@ -2,4 +2,4 @@
<li><%= icon "view-all", all_services_path, nil, nil, "View All Services" %></li>
</ul>
-<%= render :partial => "contributions/most_tabs", :locals => { :type => "BioCatService" } %>
+<%= render :partial => "contributions/most_tabs", :locals => { :type => "Service" } %>
Modified: branches/biocat/app/views/services/show.rhtml (2367 => 2368)
--- branches/biocat/app/views/services/show.rhtml 2010-03-31 12:50:51 UTC (rev 2367)
+++ branches/biocat/app/views/services/show.rhtml 2010-03-31 13:15:32 UTC (rev 2368)
@@ -123,7 +123,7 @@
<h2>Service categories</h2>
-<% @contributable.bio_cat_service_categories.each do |category| %>
+<% @contributable.service_categories.each do |category| %>
<table class="simple">
@@ -158,7 +158,7 @@
<h2>Service types</h2>
-<% @contributable.bio_cat_service_types.each do |type| %>
+<% @contributable.service_types.each do |type| %>
<table class="simple">
@@ -188,7 +188,7 @@
<h2>Service tags</h2>
-<% @contributable.bio_cat_service_tags.each do |tag| %>
+<% @contributable.service_tags.each do |tag| %>
<table class="simple">
@@ -223,7 +223,7 @@
<h2>Service deployments</h2>
-<% @contributable.bio_cat_service_deployments.each do |deployment| %>
+<% @contributable.service_deployments.each do |deployment| %>
<table class="simple">
@@ -289,37 +289,37 @@
<tr>
<td>Provider created_at</td>
- <td><%=h deployment.bio_cat_service_provider.created_at -%></td>
+ <td><%=h deployment.service_provider.created_at -%></td>
</tr>
<tr>
<td>Provider updated_at</td>
- <td><%=h deployment.bio_cat_service_provider.updated_at -%></td>
+ <td><%=h deployment.service_provider.updated_at -%></td>
</tr>
<tr>
<td>Provider retrieved_at</td>
- <td><%=h deployment.bio_cat_service_provider.retrieved_at -%></td>
+ <td><%=h deployment.service_provider.retrieved_at -%></td>
</tr>
<tr>
<td>Provider uri</td>
- <td><%=h deployment.bio_cat_service_provider.uri -%></td>
+ <td><%=h deployment.service_provider.uri -%></td>
</tr>
<tr>
<td>Provider name</td>
- <td><%=h deployment.bio_cat_service_provider.name -%></td>
+ <td><%=h deployment.service_provider.name -%></td>
</tr>
<tr>
<td>Provider description</td>
- <td><%=h deployment.bio_cat_service_provider.description -%></td>
+ <td><%=h deployment.service_provider.description -%></td>
</tr>
<tr>
<td>Provider created</td>
- <td><%=h deployment.bio_cat_service_provider.created -%></td>
+ <td><%=h deployment.service_provider.created -%></td>
</tr>
</table>
Modified: branches/biocat/config/schema.d/services.xml (2367 => 2368)
--- branches/biocat/config/schema.d/services.xml 2010-03-31 12:50:51 UTC (rev 2367)
+++ branches/biocat/config/schema.d/services.xml 2010-03-31 13:15:32 UTC (rev 2368)
@@ -3,7 +3,7 @@
<!-- BioCatalogue services -->
- <table name="bio_cat_services">
+ <table name="services">
<column type="integer" name="contributor_id"/>
<column type="string" name="contributor_type"/>
@@ -41,63 +41,63 @@
<column type="string" name="monitor_small_symbol_url"/>
<column type="datetime" name="monitor_last_checked"/>
- <has-many target="bio_cat_service_categories"/>
- <has-many target="bio_cat_service_types"/>
- <has-many target="bio_cat_service_tags"/>
- <has-many target="bio_cat_service_deployments"/>
+ <has-many target="service_categories"/>
+ <has-many target="service_types"/>
+ <has-many target="service_tags"/>
+ <has-many target="service_deployments"/>
</table>
<!-- BioCatalogue service categories -->
- <table name="bio_cat_service_categories">
+ <table name="service_categories">
<column type="datetime" name="created_at"/>
<column type="datetime" name="updated_at"/>
<column type="datetime" name="retrieved_at"/>
- <column type="integer" name="bio_cat_service_id"/>
+ <column type="integer" name="service_id"/>
<column type="string" name="uri"/>
<column type="string" name="label"/>
- <belongs-to target="bio_cat_service"/>
+ <belongs-to target="service"/>
</table>
<!-- BioCatalogue service types -->
- <table name="bio_cat_service_types">
+ <table name="service_types">
<column type="datetime" name="created_at"/>
<column type="datetime" name="updated_at"/>
<column type="datetime" name="retrieved_at"/>
- <column type="integer" name="bio_cat_service_id"/>
+ <column type="integer" name="service_id"/>
<column type="string" name="label"/>
- <belongs-to target="bio_cat_service"/>
+ <belongs-to target="service"/>
</table>
<!-- BioCatalogue service tags -->
- <table name="bio_cat_service_tags">
+ <table name="service_tags">
<column type="datetime" name="created_at"/>
<column type="datetime" name="updated_at"/>
<column type="datetime" name="retrieved_at"/>
- <column type="integer" name="bio_cat_service_id"/>
+ <column type="integer" name="service_id"/>
<column type="string" name="uri"/>
<column type="string" name="label"/>
- <belongs-to target="bio_cat_service"/>
+ <belongs-to target="service"/>
</table>
<!-- BioCatalogue service deployments -->
- <table name="bio_cat_service_deployments">
+ <table name="service_deployments">
<column type="datetime" name="created_at"/>
<column type="datetime" name="updated_at"/>
@@ -116,17 +116,17 @@
<column type="datetime" name="created"/>
- <column type="integer" name="bio_cat_service_id"/>
- <column type="integer" name="bio_cat_service_provider_id"/>
+ <column type="integer" name="service_id"/>
+ <column type="integer" name="service_provider_id"/>
- <belongs-to target="bio_cat_service_provider"/>
- <belongs-to target="bio_cat_service"/>
+ <belongs-to target="service_provider"/>
+ <belongs-to target="service"/>
</table>
<!-- BioCatalogue service providers -->
- <table name="bio_cat_service_providers">
+ <table name="service_providers">
<column type="datetime" name="created_at"/>
<column type="datetime" name="updated_at"/>
@@ -138,7 +138,7 @@
<column type="datetime" name="created"/>
- <has-many target="bio_cat_service_deployments" foreign_key="bio_cat_service_provider_id"/>
+ <has-many target="service_deployments" foreign_key="service_provider_id"/>
</table>
Modified: branches/biocat/lib/bio_catalogue_import.rb (2367 => 2368)
--- branches/biocat/lib/bio_catalogue_import.rb 2010-03-31 12:50:51 UTC (rev 2367)
+++ branches/biocat/lib/bio_catalogue_import.rb 2010-03-31 13:15:32 UTC (rev 2368)
@@ -80,7 +80,7 @@
annotations_element = LibXML::XML::Parser.string(fetch_uri(annotations_uri)).parse.root
monitoring_element = LibXML::XML::Parser.string(fetch_uri(monitoring_uri)).parse.root
- service = BioCatService.create(
+ service = Service.create(
:retrieved_at => uri_retrieved_at(service_uri),
:contributor => @federation_source,
@@ -114,26 +114,26 @@
service.contribution.save
summary_element.find('/bc:service/bc:summary/bc:category', @@biocat_ns).each do |category_element|
- BioCatServiceCategory.create(
- :bio_cat_service => service,
- :retrieved_at => uri_retrieved_at(summary_uri),
- :uri => get_link(category_element, '@xlink:href'),
- :label => get_text(category_element, 'text()'))
+ ServiceCategory.create(
+ :service => service,
+ :retrieved_at => uri_retrieved_at(summary_uri),
+ :uri => get_link(category_element, '@xlink:href'),
+ :label => get_text(category_element, 'text()'))
end
summary_element.find('/bc:service/bc:summary/bc:serviceType', @@biocat_ns).each do |category_element|
- BioCatServiceType.create(
- :bio_cat_service => service,
- :retrieved_at => uri_retrieved_at(summary_uri),
- :label => get_text(category_element, 'text()'))
+ ServiceType.create(
+ :service => service,
+ :retrieved_at => uri_retrieved_at(summary_uri),
+ :label => get_text(category_element, 'text()'))
end
summary_element.find('/bc:service/bc:summary/bc:tag', @@biocat_ns).each do |tag_element|
- BioCatServiceTag.create(
- :bio_cat_service => service,
- :retrieved_at => uri_retrieved_at(summary_uri),
- :uri => get_link(tag_element, '@xlink:href'),
- :label => get_text(tag_element, 'text()'))
+ ServiceTag.create(
+ :service => service,
+ :retrieved_at => uri_retrieved_at(summary_uri),
+ :uri => get_link(tag_element, '@xlink:href'),
+ :label => get_text(tag_element, 'text()'))
end
# deployments and providers
@@ -143,10 +143,10 @@
deployment_uri = get_link(deployment_element, '@xlink:href')
provider_uri = get_link(deployment_element, 'bc:serviceProvider/@xlink:href')
- next if BioCatServiceDeployment.find_by_uri(deployment_uri)
+ next if ServiceDeployment.find_by_uri(deployment_uri)
- if BioCatServiceProvider.find_by_uri(provider_uri).nil?
- BioCatServiceProvider.create(
+ if ServiceProvider.find_by_uri(provider_uri).nil?
+ ServiceProvider.create(
:uri => provider_uri,
:retrieved_at => uri_retrieved_at(service_uri),
:name => get_text(deployment_element, 'bc:serviceProvider/bc:name/text()'),
@@ -154,35 +154,27 @@
:created => get_text(deployment_element, 'bc:serviceProvider/dcterms:created/text()'))
end
- provider = BioCatServiceProvider.find_by_uri(provider_uri)
+ provider = ServiceProvider.find_by_uri(provider_uri)
- deployment = BioCatServiceDeployment.create(
- :bio_cat_service => service,
- :bio_cat_service_provider => provider,
- :retrieved_at => uri_retrieved_at(service_uri),
- :uri => get_link(deployment_element, '@xlink:href'),
- :endpoint => get_text(deployment_element, 'bc:endpoint/text()'),
- :city => get_text(deployment_element, 'bc:location/bc:city/text()'),
- :country => get_text(deployment_element, 'bc:location/bc:country/text()'),
- :iso3166_country_code => get_text(deployment_element, 'bc:location/bc:iso3166CountryCode/text()'),
- :flag_url => get_link(deployment_element, 'bc:location/bc:flag/@xlink:href'),
- :submitter_label => get_attr(deployment_element, 'bc:submitter/@resourceName'),
- :submitter_uri => get_attr(deployment_element, 'bc:submitter/@xlink:href'),
- :created => get_text(deployment_element, 'dcterms:created/text()'))
+ deployment = ServiceDeployment.create(
+ :service => service,
+ :service_provider => provider,
+ :retrieved_at => uri_retrieved_at(service_uri),
+ :uri => get_link(deployment_element, '@xlink:href'),
+ :endpoint => get_text(deployment_element, 'bc:endpoint/text()'),
+ :city => get_text(deployment_element, 'bc:location/bc:city/text()'),
+ :country => get_text(deployment_element, 'bc:location/bc:country/text()'),
+ :iso3166_country_code => get_text(deployment_element, 'bc:location/bc:iso3166CountryCode/text()'),
+ :flag_url => get_link(deployment_element, 'bc:location/bc:flag/@xlink:href'),
+ :submitter_label => get_attr(deployment_element, 'bc:submitter/@resourceName'),
+ :submitter_uri => get_attr(deployment_element, 'bc:submitter/@xlink:href'),
+ :created => get_text(deployment_element, 'dcterms:created/text()'))
end
end
def self.import_biocatalogue_services(uri)
- Contribution.delete_all("contributable_type = 'BioCatService'")
- BioCatService.delete_all
- BioCatServiceCategory.delete_all
- BioCatServiceType.delete_all
- BioCatServiceTag.delete_all
- BioCatServiceDeployment.delete_all
- BioCatServiceProvider.delete_all
-
while true
doc = LibXML::XML::Parser.string(fetch_uri(uri)).parse.root