metamri 0.1.21 → 0.1.22

data/VERSION

@@ -1 +1 @@
-0.1.21
+0.1.22

data/bin/list_visit

@@ -51,7 +51,14 @@ end
 def list_visit(raw_directory, options = {})
   unless $LOG
     $LOG = Logger.new(STDOUT)
-    $LOG.level = options[:verbose] ? Logger::DEBUG : Logger::INFO
+    case options[:verbose]
+    when true
+      $LOG.level = Logger::DEBUG
+    when nil 
+      $LOG.level = Logger::INFO
+    when false
+      $LOG.level = Logger::WARN
+    end
   end
   
   # First try to lookup Visit and Datasets through active_resource
@@ -65,7 +72,7 @@ def list_visit(raw_directory, options = {})
     raise IOError.new("Could not lookup visit using path.") unless visit
     raise IOError.new("Returned visit does not match path.") unless visit.path == raw_directory
   rescue ScriptError, IOError => e
-    puts e
+    puts e unless options[:verbose] == false
     visit = VisitRawDataDirectory.new(raw_directory)
     begin
       visit.scan(options)
@@ -78,7 +85,15 @@ def list_visit(raw_directory, options = {})
   # Output a pretty version of the visit details.
   # Visit is Either a RawVisitDataDirectory or a RawVisitDataDirectoryResource,
   # and either should respond to to_s
-  visit.to_s
+  #
+  # Either output the entire visit (or if a search is requested) just the 
+  # datasets that match the search.
+  unless options[:grep]
+    visit.to_s
+  else
+    datasets = visit.datasets.select{ |ds| ds.series_description =~ /#{options[:grep]}/i }
+    puts datasets.collect {|ds| ds.methods.include?('directory') ? ds.directory : ds.path }
+  end
 
 end
 
@@ -95,6 +110,11 @@ def parse_options
       options[:verbose] = true
     end
     
+    opts.on('-g', '--grep GREP', "Search series descriptions") do |grep|
+      options[:grep] = grep
+      options[:verbose] = false
+    end
+    
     opts.on_tail('-h', '--help',          "Show this message")          { puts(parser); exit }
     opts.on_tail("If no directory is given, default is the current directory.")
     opts.on_tail("Example: #{File.basename(__FILE__)} pd006")

data/metamri.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{metamri}
-  s.version = "0.1.21"
+  s.version = "0.1.22"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Kristopher J. Kosmatka"]
-  s.date = %q{2010-07-15}
+  s.date = %q{2010-10-05}
   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"]
@@ -50,7 +50,7 @@ Gem::Specification.new do |s|
   s.homepage = %q{http://github.com/brainmap/metamri}
   s.rdoc_options = ["--charset=UTF-8"]
   s.require_paths = ["lib"]
-  s.rubygems_version = %q{1.3.7}
+  s.rubygems_version = %q{1.3.6}
   s.summary = %q{MRI metadata}
   s.test_files = [
     "test/nifti_builder_spec.rb",
@@ -65,7 +65,7 @@ Gem::Specification.new do |s|
     current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
     s.specification_version = 3
 
-    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+    if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<sqlite3-ruby>, [">= 0"])
       s.add_runtime_dependency(%q<dicom>, [">= 0"])
       s.add_development_dependency(%q<rspec>, [">= 0"])

metadata

@@ -1,13 +1,12 @@
 --- !ruby/object:Gem::Specification 
 name: metamri
 version: !ruby/object:Gem::Version 
-  hash: 49
   prerelease: false
   segments: 
   - 0
   - 1
-  - 21
-  version: 0.1.21
+  - 22
+  version: 0.1.22
 platform: ruby
 authors: 
 - Kristopher J. Kosmatka
@@ -15,18 +14,16 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-07-15 00:00:00 -05:00
+date: 2010-10-05 00:00:00 -05:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: sqlite3-ruby
   prerelease: false
   requirement: &id001 !ruby/object:Gem::Requirement 
-    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        hash: 3
         segments: 
         - 0
         version: "0"
@@ -36,11 +33,9 @@ dependencies:
   name: dicom
   prerelease: false
   requirement: &id002 !ruby/object:Gem::Requirement 
-    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        hash: 3
         segments: 
         - 0
         version: "0"
@@ -50,11 +45,9 @@ dependencies:
   name: rspec
   prerelease: false
   requirement: &id003 !ruby/object:Gem::Requirement 
-    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        hash: 3
         segments: 
         - 0
         version: "0"
@@ -112,27 +105,23 @@ rdoc_options:
 require_paths: 
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement 
-  none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: 3
       segments: 
       - 0
       version: "0"
 required_rubygems_version: !ruby/object:Gem::Requirement 
-  none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: 3
       segments: 
       - 0
       version: "0"
 requirements: []
 
 rubyforge_project: 
-rubygems_version: 1.3.7
+rubygems_version: 1.3.6
 signing_key: 
 specification_version: 3
 summary: MRI metadata