metamri 0.1.11 → 0.1.13

data/Rakefile

@@ -27,6 +27,8 @@ begin
     gemspec.email = "kk4@medicine.wisc.edu"
     gemspec.homepage = "http://github.com/brainmap/metamri"
     gemspec.authors = ["Kristopher J. Kosmatka"]
+    gemspec.add_dependency('sqlite3-ruby')
+    gemspec.add_development_dependency('rspec')
   end
   Jeweler::GemcutterTasks.new
 rescue LoadError

data/VERSION

@@ -1 +1 @@
-0.1.11
+0.1.13

data/bin/list_visit

@@ -35,26 +35,40 @@ $:.unshift File.join(File.dirname(__FILE__),'..','lib')
 require 'metamri'
 require 'pathname'
 require 'rdoc/usage'
-require 'logger'
+# require 'logger'
 
 def list_visit(raw_directory)
-  $LOG = Logger.new(STDOUT)  
-  $LOG.level = Logger::INFO
-  visit = VisitRawDataDirectory.new(raw_directory)
-  # visit = VisitRawDataDirectoryResource.find(:all, :from => '/visits/found.xml', :params => {:visit_search => {:rmr => 'rmr'}})
-
+  # $LOG = Logger.new(STDOUT)
+  # $LOG.level = Logger::INFO
+  
+  # First try to lookup Visit and Datasets through active_resource
+  # Then fall back to scanning them fresh.
+  
   begin
-    visit.scan
-    # visit.datasets = RawImageDatasetResource.find(:all, :from => "/visits/#{visit.database_id}/image_datasets.xml" )
-  rescue IndexError => e
-    $LOG.error "Are you sure #{raw_directory} is a valid raw visit directory?"
-    raise e
+    # raise
+    visit = VisitRawDataDirectoryResource.find(:first, :params => {:search => {:path => raw_directory}})
+    raise "Could not lookup visit using path." unless visit
+    raise "Incorrect visit found." unless visit.path == raw_directory
   rescue Exception => e
-    $LOG.error "There was a problem scanning a dataset in #{visit.visit_directory}... skipping."
-    $LOG.error "Exception message: #{e.message}"
-    raise e
+    puts e
+    visit = VisitRawDataDirectory.new(raw_directory)
+    begin
+      visit.scan
+    rescue IndexError => e
+      $LOG.error "Are you sure #{raw_directory} is a valid raw visit directory?"
+      raise e
+    end
   end
+
+  # begin
+  # rescue Exception => e
+  #   $LOG.error "There was a problem scanning a dataset in #{visit.visit_directory}... skipping."
+  #   $LOG.error "Exception message: #{e.message}"
+  #   raise e
+  # end
   
+  # Visit is Either a RawVisitDataDirectory or a RawVisitDataDirectoryResource
+  # Either can handle printing to_s
   visit.to_s
 
 end
@@ -63,7 +77,8 @@ if File.basename(__FILE__) == File.basename($PROGRAM_NAME)
   RDoc::usage() if (ARGV[0] == '-h')
 
   # Default to scanning the current directory if no argument was given.
-  raw_directory = ARGV[0] ||= File.expand_path('.')
+  raw_directory = ARGV[0] ||= Dir.pwd
+  raw_directory = File.expand_path(raw_directory)
 
   list_visit(raw_directory)
 end

data/lib/metamri/raw_image_dataset_resource.rb

@@ -7,7 +7,7 @@ class RawImageDatasetResource < ActiveResource::Base
   # Creates a Backwards Transfer to go from ActiveRecord to Metamri Classes
   # ActiveResource will provide :attr methods for column names from the database, 
   # so check the current schema.rb file for those.
-  def to_metamri_image_dataset
+  def to_metamri_raw_image_dataset
     # A Metamri Class requires at least one valid image file.
     # This is a little tricky since we really only care about the variables, not rescanning them.
     
@@ -17,4 +17,16 @@ class RawImageDatasetResource < ActiveResource::Base
     
     return @dataset
   end
+  
+  # Map RawImageDatasetResource and RawImageDataset
+  # def method_missing(m, *args, &block)
+  #   puts m
+  #   if m == :directory
+  #     path
+  #   elsif m == :directory_basename
+  #     File.basename(directory)
+  #   else
+  #     super
+  #   end
+  # end
 end

data/lib/metamri/visit_raw_data_directory_resource.rb

@@ -1,6 +1,7 @@
-require 'active_resource'
+$:.unshift File.dirname(__FILE__)
 
-DATAPANDA_SERVER = 'http://144.92.151.228'
+require 'active_resource'
+require 'raw_image_dataset_resource'
 
 class VisitRawDataDirectoryResource < ActiveResource::Base
   self.site = VisitRawDataDirectory::DATAPANDA_SERVER
@@ -17,4 +18,15 @@ class VisitRawDataDirectoryResource < ActiveResource::Base
     @visit.database_id = id
     return @visit
   end
-end
+  
+  def datasets
+    @datasets ||= RawImageDatasetResource.find(:all, :from => "/visits/#{id}/image_datasets.xml" )
+  end
+  
+  def to_s
+    metamri_visit = to_metamri_visit_raw_data_directory
+    metamri_visit.datasets = datasets.collect { |ds| ds.to_metamri_raw_image_dataset}
+    metamri_visit.to_s
+  end
+end
+

data/metamri.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{metamri}
-  s.version = "0.1.11"
+  s.version = "0.1.13"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Kristopher J. Kosmatka"]
-  s.date = %q{2010-02-03}
+  s.date = %q{2010-02-04}
   s.description = %q{Extraction of MRI metadata and insertion into compatible sqlite3 databases.}
   s.email = %q{kk4@medicine.wisc.edu}
   s.executables = ["import_study.rb", "import_visit.rb", "import_respiratory_files.rb", "list_visit", "convert_visit.rb"]
@@ -63,9 +63,15 @@ Gem::Specification.new do |s|
     s.specification_version = 3
 
     if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<sqlite3-ruby>, [">= 0"])
+      s.add_development_dependency(%q<rspec>, [">= 0"])
     else
+      s.add_dependency(%q<sqlite3-ruby>, [">= 0"])
+      s.add_dependency(%q<rspec>, [">= 0"])
     end
   else
+    s.add_dependency(%q<sqlite3-ruby>, [">= 0"])
+    s.add_dependency(%q<rspec>, [">= 0"])
   end
 end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: metamri
 version: !ruby/object:Gem::Version 
-  version: 0.1.11
+  version: 0.1.13
 platform: ruby
 authors: 
 - Kristopher J. Kosmatka
@@ -9,10 +9,29 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-02-03 00:00:00 -06:00
+date: 2010-02-04 00:00:00 -06:00
 default_executable: 
-dependencies: []
-
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: sqlite3-ruby
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: rspec
+  type: :development
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+    version: 
 description: Extraction of MRI metadata and insertion into compatible sqlite3 databases.
 email: kk4@medicine.wisc.edu
 executables: