opentox-ruby 3.0.0 → 3.0.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/ChangeLog +5 -0
- data/VERSION +1 -1
- data/lib/authorization.rb +1 -1
- data/lib/ontology.rb +16 -27
- metadata +6 -4
data/ChangeLog
ADDED
data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
3.0.
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1
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+
3.0.1
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data/lib/authorization.rb
CHANGED
@@ -319,7 +319,7 @@ module OpenTox
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# if policy exists check for POST rights
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if authorize(uri, "POST", subjectid)
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true
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-
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else
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LOGGER.error "OpenTox::Authorization.check_policy, already exists, but no POST-authorization with subjectid: #{subjectid}"
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false
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end
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data/lib/ontology.rb
CHANGED
@@ -4,13 +4,9 @@ module OpenTox
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def self.querystring(classname="Endpoints")
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return CGI.escape("PREFIX ot:<http://www.opentox.org/api/1.1#>
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PREFIX ota:<http://www.opentox.org/algorithms.owl#>
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PREFIX owl:<http://www.w3.org/2002/07/owl#>
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PREFIX dc:<http://purl.org/dc/elements/1.1/>
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PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
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PREFIX otee:<http://www.opentox.org/echaEndpoints.owl#>
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PREFIX toxcast:<http://www.opentox.org/toxcast.owl#>
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select *
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where {
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?endpoint rdfs:subClassOf otee:#{classname}.
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@@ -18,25 +14,22 @@ module OpenTox
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}")
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end
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-
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-
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-
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-
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# Gets Endpoint name of a specific endpoint URI
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# @param [String] endpointuri e.G. "http://www.opentox.org/echaEndpoints.owl#EcotoxicEffects"
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# @return [String] endpointname: e.G.: "Ecotoxic effects"
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def self.get_endpoint_name(endpointuri)
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qstring = CGI.escape("PREFIX dc:<http://purl.org/dc/elements/1.1/>
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select distinct ?title
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where {
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?endpoint dc:title ?title.
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FILTER (?endpoint = <#{endpointuri}>)
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}")
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begin
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RestClientWrapper.get("#{ONTOLOGY_SERVER}?query=#{qstring}",:accept => "text/csv").collect{|l| l.gsub("\r\n", "") if l.to_s != "title\r\n"}.uniq.compact.sort.first.to_s
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rescue
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LOGGER.warn "OpenTox::Ontology::Echa.get_endpoint_name(#{endpointuri}) ontology service is not reachable."
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[]
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end
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-
return out
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end
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def self.endpoint_option_list(include_blank=true)
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out = "<select id='endpoint' name='endpoint'>\n"
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out += "<option value='' id='please_select'>Please select</option>\n" if include_blank
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out += make_option_list
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out += "</select>\n"
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return out
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end
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# Gets Endpoints of specific level from ontology service
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@@ -115,11 +108,8 @@ module OpenTox
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# Query string to find a registered model
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# @param [String] uri, model URI
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def self.querystring(uri)
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return CGI.escape("PREFIX
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PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
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PREFIX owl:<http://www.w3.org/2002/07/owl#>
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return CGI.escape("PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
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PREFIX dc:<http://purl.org/dc/elements/1.1/>
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PREFIX dcterms:<http://purl.org/dc/terms/>
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PREFIX ot:<http://www.opentox.org/api/1.1#>
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select distinct ?model ?title ?creator ?trainingDataset ?algorithm
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where {
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@@ -132,6 +122,5 @@ module OpenTox
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}")
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end
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end
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-
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end
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end
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metadata
CHANGED
@@ -1,13 +1,13 @@
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1
1
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--- !ruby/object:Gem::Specification
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name: opentox-ruby
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version: !ruby/object:Gem::Version
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hash:
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hash: 5
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prerelease:
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segments:
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- 3
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- 0
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-
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version: 3.0.
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- 1
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version: 3.0.1
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platform: ruby
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authors:
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- Christoph Helma, Martin Guetlein, Andreas Maunz, Micha Rautenberg, David Vorgrimmler
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@@ -15,7 +15,7 @@ autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2011-
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date: 2011-10-24 00:00:00 +02:00
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default_executable:
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dependencies:
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- !ruby/object:Gem::Dependency
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@@ -536,9 +536,11 @@ executables: []
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extensions: []
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extra_rdoc_files:
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+
- ChangeLog
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- LICENSE
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- README.markdown
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files:
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- ChangeLog
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- LICENSE
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- README.markdown
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- Rakefile
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