t2-server 0.6.1 → 0.9.0

data/lib/t2-server/util.rb

@@ -0,0 +1,71 @@
+# Copyright (c) 2010-2012 The University of Manchester, UK.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+#  * Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+#
+#  * Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#
+#  * Neither the names of The University of Manchester nor the names of its
+#    contributors may be used to endorse or promote products derived from this
+#    software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# Author: Robert Haines
+
+module T2Server
+  module Util
+
+    # :call-seq:
+    #   Util.strip_uri_credentials(uri) -> URI, Credentials
+    #
+    # Strip user credentials from an address in URI or String format and return
+    # a tuple of the URI minus the credentials and a T2Server::Credentials
+    # object.
+    def self.strip_uri_credentials(uri)
+      # we want to use URIs here but strings can be passed in
+      unless uri.is_a? URI
+        uri = URI.parse(Util.strip_path_slashes(uri))
+      end
+
+      creds = nil
+
+      # strip username and password from the URI if present
+      if uri.user != nil
+        creds = T2Server::HttpBasic.new(uri.user, uri.password)
+
+        uri = URI::HTTP.new(uri.scheme, nil, uri.host, uri.port, nil,
+        uri.path, nil, nil, nil);
+      end
+
+      [uri, creds]
+    end
+
+    # :call-seq:
+    #   Util.strip_path_slashes(path) -> String
+    #
+    # Returns a new String with one leading and one trailing slash
+    # removed from the ends of _path_ (if present).
+    def self.strip_path_slashes(path)
+      path.gsub(/^\//, "").chomp("/")
+    end
+
+  end
+end

data/lib/t2-server/xml/libxml.rb

@@ -0,0 +1,87 @@
+# Copyright (c) 2010-2012 The University of Manchester, UK.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+#  * Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+#
+#  * Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#
+#  * Neither the names of The University of Manchester nor the names of its
+#    contributors may be used to endorse or promote products derived from this
+#    software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# Author: Robert Haines
+
+require 'rubygems'
+require 'libxml'
+
+module T2Server
+  module XML
+    # Shut the libxml error handler up
+    LibXML::XML::Error.set_handler(&LibXML::XML::Error::QUIET_HANDLER)
+
+    module Methods
+      def xml_document(string)
+        LibXML::XML::Document.string(string)
+      end
+
+      def xml_text_node(text)
+        LibXML::XML::Node.new_text(text)
+      end
+
+      def xml_first_child(node)
+        node.first
+      end
+
+      def xml_children(doc, &block)
+        doc.each { |node| yield node }
+      end
+
+      def xml_node_name(node)
+        node.name
+      end
+
+      def xml_node_content(node)
+        node.content
+      end
+
+      def xml_node_attribute(node, attribute)
+        node.attributes[attribute]
+      end
+
+      def xpath_compile(xpath)
+        LibXML::XML::XPath::Expression.new(xpath)
+      end
+
+      def xpath_find(doc, expr)
+        doc.find(expr, Namespaces::MAP)
+      end
+
+      def xpath_first(doc, expr)
+        doc.find_first(expr, Namespaces::MAP)
+      end
+
+      def xpath_attr(doc, expr, attribute)
+        doc.find_first(expr, Namespaces::MAP).attributes[attribute]
+      end
+    end
+  end
+end

data/lib/t2-server/xml/nokogiri.rb

@@ -0,0 +1,85 @@
+# Copyright (c) 2010-2012 The University of Manchester, UK.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+#  * Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+#
+#  * Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#
+#  * Neither the names of The University of Manchester nor the names of its
+#    contributors may be used to endorse or promote products derived from this
+#    software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# Author: Robert Haines
+
+require 'rubygems'
+require 'nokogiri'
+
+module T2Server
+  module XML
+
+    module Methods
+      def xml_document(string)
+        Nokogiri::XML(string)
+      end
+
+      def xml_text_node(text)
+        Nokogiri::XML::Text.new(text, Nokogiri::XML::Document.new).to_s
+      end
+
+      def xml_first_child(node)
+        node.first_element_child
+      end
+
+      def xml_children(doc, &block)
+        doc.children.each &block
+      end
+
+      def xml_node_name(node)
+        node.node_name
+      end
+
+      def xml_node_content(node)
+        node.content
+      end
+
+      def xml_node_attribute(node, attribute)
+        node[attribute]
+      end
+
+      def xpath_compile(xpath)
+        xpath
+      end
+
+      def xpath_find(doc, expr)
+        doc.xpath(expr, Namespaces::MAP)
+      end
+
+      def xpath_first(doc, expr)
+        doc.at_xpath(expr, Namespaces::MAP)
+      end
+
+      def xpath_attr(doc, expr, attribute)
+        doc.at_xpath(expr, Namespaces::MAP)[attribute]
+      end
+    end
+  end
+end

data/lib/t2-server/xml/rexml.rb

@@ -0,0 +1,85 @@
+# Copyright (c) 2010-2012 The University of Manchester, UK.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+#  * Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+#
+#  * Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#
+#  * Neither the names of The University of Manchester nor the names of its
+#    contributors may be used to endorse or promote products derived from this
+#    software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# Author: Robert Haines
+
+require 'rexml/document'
+require 'rexml/text'
+
+module T2Server
+  module XML
+
+    module Methods
+      def xml_document(string)
+        REXML::Document.new(string)
+      end
+
+      def xml_text_node(text)
+        REXML::Text.new(text).to_s
+      end
+
+      def xml_first_child(node)
+        node.first
+      end
+
+      def xml_children(doc, &block)
+        doc.each { |node| yield node }
+      end
+
+      def xml_node_name(node)
+        node.name
+      end
+
+      def xml_node_content(node)
+        node.text
+      end
+
+      def xml_node_attribute(node, attribute)
+        node.attributes[attribute]
+      end
+
+      def xpath_compile(xpath)
+        xpath
+      end
+
+      def xpath_find(doc, expr)
+        REXML::XPath.each(doc, expr, Namespaces::MAP)
+      end
+
+      def xpath_first(doc, expr)
+        REXML::XPath.first(doc, expr, Namespaces::MAP)
+      end
+
+      def xpath_attr(doc, expr, attribute)
+        REXML::XPath.first(doc, expr, Namespaces::MAP).attributes[attribute]
+      end
+    end
+  end
+end

data/lib/t2-server/xml/xml.rb

@@ -0,0 +1,111 @@
+# Copyright (c) 2010-2012 The University of Manchester, UK.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+#  * Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+#
+#  * Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#
+#  * Neither the names of The University of Manchester nor the names of its
+#    contributors may be used to endorse or promote products derived from this
+#    software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# Author: Robert Haines
+
+begin
+  require 't2-server/xml/libxml'
+rescue LoadError
+  begin
+    require 't2-server/xml/nokogiri'
+  rescue LoadError
+    require 't2-server/xml/rexml'
+  end
+end
+
+module T2Server
+  module XML
+
+    module Namespaces
+      SERVER = "http://ns.taverna.org.uk/2010/xml/server/"
+      REST   = SERVER + "rest/"
+      ADMIN  = SERVER + "admin/"
+      PORT   = "http://ns.taverna.org.uk/2010/port/"
+
+      MAP    = {
+        "nss"  => Namespaces::SERVER,
+        "nsr"  => Namespaces::REST,
+        "nsa"  => Namespaces::ADMIN,
+        "port" => Namespaces::PORT
+      }
+    end
+
+    module Fragments
+      WORKFLOW      = "<t2s:workflow xmlns:t2s=\"#{Namespaces::SERVER}\">\n" +
+                      "  %s\n</t2s:workflow>"
+      RUNINPUT      = "<t2sr:runInput xmlns:t2sr=\"#{Namespaces::REST}\">\n" +
+                      "  %s\n</t2sr:runInput>"
+      RUNINPUTVALUE = RUNINPUT % "<t2sr:value>%s</t2sr:value>"
+      RUNINPUTFILE  = RUNINPUT % "<t2sr:file>%s</t2sr:file>"
+      UPLOAD        = "<t2sr:upload xmlns:t2sr=\"#{Namespaces::REST}\" " +
+                        "t2sr:name=\"%s\">\n  %s\n</t2sr:upload>"
+      MKDIR         = "<t2sr:mkdir xmlns:t2sr=\"#{Namespaces::REST}\" " +
+                        "t2sr:name=\"%s\" />"
+
+      PERMISSION    = "<t2sr:userName>%s</t2sr:userName>" +
+                      "<t2sr:permission>%s</t2sr:permission>"
+      PERM_UPDATE   = "<t2sr:permissionUpdate " +
+                      "xmlns:t2sr=\"#{Namespaces::REST}\">" +
+                      "#{PERMISSION}</t2sr:permissionUpdate>"
+
+      SERVICE_URI   = "<t2s:serviceURI>%s</t2s:serviceURI>"
+      CREDENTIAL    = "<t2sr:credential xmlns:t2sr=\"#{Namespaces::REST}\"" +
+                        " xmlns:t2s=\"#{Namespaces::SERVER}\">\n" +
+                      "%s\n</t2sr:credential>"
+      USERPASS_CRED = "<t2s:userpass>\n" +
+                      "  #{SERVICE_URI}\n" +
+                      "  <t2s:username>%s</t2s:username>\n" +
+                      "  <t2s:password>%s</t2s:password>\n" +
+                      "</t2s:userpass>"
+
+      KEYPAIR_CRED  = "<t2s:keypair>\n" +
+                      "  #{SERVICE_URI}\n" +
+                      "  <t2s:credentialName>%s</t2s:credentialName>\n" +
+                      "  <t2s:credentialBytes>%s</t2s:credentialBytes>\n" +
+                      "  <t2s:fileType>%s</t2s:fileType>\n" +
+                      "  <t2s:unlockPassword>%s</t2s:unlockPassword>\n" +
+                      "</t2s:keypair>"
+
+      TRUST         = "<t2s:trustedIdentity " +
+                        "xmlns:t2s=\"#{Namespaces::SERVER}\">\n" +
+                      "  <t2s:certificateBytes>%s</t2s:certificateBytes>\n" +
+                      "  <t2s:fileType>%s</t2s:fileType>\n" +
+                      "</t2s:trustedIdentity>"
+    end
+
+    module Methods
+      # The methods in this namespace are provided by the particular XML
+      # library selected above. The xpath_compile method needs to be declared
+      # as a module method so it can be used as a class method when it is
+      # mixed in.
+      module_function :xpath_compile
+    end
+  end
+end

data/lib/t2server.rb

@@ -14,7 +14,7 @@
 #
 #  * Neither the names of The University of Manchester nor the names of its
 #    contributors may be used to endorse or promote products derived from this
-#    software without specific prior written permission. 
+#    software without specific prior written permission.
 #
 # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 # AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
@@ -32,4 +32,7 @@
 
 # This is simply here to provide backwards compatibility. Old versions had an
 # inconsistancy between the gem name and the file to require to use it.
+warn "[DEPRECATION] Code should no longer require 't2server'. Please use " +
+  "require 't2-server' as this is consistent with the gem name. In version " +
+  "1.0 require 't2server' will cease to work."
 require 't2-server'