metamri 0.1.18 → 0.1.19

data/VERSION

@@ -1 +1 @@
-0.1.18
+0.1.19

data/bin/list_visit

@@ -33,29 +33,42 @@
 
 $:.unshift File.join(File.dirname(__FILE__),'..','lib')
 
-require 'metamri'
 require 'pathname'
-require 'rdoc/usage'
-# require 'logger'
+require 'logger'
+require 'metamri'
 
-def list_visit(raw_directory)
+def run!
+  options = parse_options
+  
+  # Default to scanning the current directory if no argument was given.
+  raw_directory = ARGV[0] ||= Dir.pwd
+  raw_directory = File.expand_path(raw_directory)
+  
+  list_visit raw_directory, options
+  
+end
+
+def list_visit(raw_directory, options = {})
   unless $LOG
     $LOG = Logger.new(STDOUT)
-    $LOG.level = Logger::INFO
+    $LOG.level = options[:verbose] ? Logger::DEBUG : Logger::INFO
   end
   
   # First try to lookup Visit and Datasets through active_resource
   # Then fall back to scanning them fresh using the metamri classes.
   
   begin
+    raise ScriptError, "Scaning filesystem directly..." if options[:force_scan]
+    
     visit = VisitRawDataDirectoryResource.find(:first, :params => {:search => {:path => raw_directory}})
+    
     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 IOError => e
+  rescue ScriptError, IOError => e
     puts e
     visit = VisitRawDataDirectory.new(raw_directory)
     begin
-      visit.scan
+      visit.scan(options)
     rescue IndexError => e
       $LOG.error "Are you sure #{raw_directory} is a valid raw visit directory?"
       raise e
@@ -69,12 +82,29 @@ def list_visit(raw_directory)
 
 end
 
-if File.basename(__FILE__) == File.basename($PROGRAM_NAME)
-  RDoc::usage() if (ARGV[0] == '-h')
+def parse_options
+  options = Hash.new
+  parser = OptionParser.new do |opts|
+    opts.banner = "Usage: #{File.basename(__FILE__)} [options] [directory]"
 
-  # Default to scanning the current directory if no argument was given.
-  raw_directory = ARGV[0] ||= Dir.pwd
-  raw_directory = File.expand_path(raw_directory)
+    opts.on('-s', '--scan', "Scan filesystem directly instead of checking database first.") do
+      options[:force_scan] = true
+    end
+    
+    opts.on('-v', '--verbose', "Be wordy.") do
+      options[:verbose] = true
+    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")
 
-  list_visit(raw_directory)
+  end
+  parser.parse!(ARGV)
+
+  return options
+end
+
+if File.basename(__FILE__) == File.basename($PROGRAM_NAME)
+  run!
 end

data/lib/metamri/core_additions.rb

@@ -92,6 +92,25 @@ class Pathname
     return
   end
   
+  def recursive_local_copy(ignore_patterns = [], &block)
+    tempdir = Dir.mktmpdir('local_orig')
+
+    entries.each do |leaf|
+      branch = self + leaf
+      next if branch.directory?
+      next if ignore_patterns.collect { |pat| leaf.to_s =~ pattern } 
+      next if branch.should_be_skipped
+      lc = branch.local_copy(tempdir)
+      lc.chmod(0444 | 0200 | 0020 )
+    end
+    
+    return tempdir
+  end
+  
+  def should_be_skipped
+    self.to_s =~ /^\./ || self.symlink?
+  end
+  
 =begin
   Creates a local, unzipped copy of a file for use in scanning.
   Will return a pathname to the local copy if called directly, or can also be 

data/lib/metamri/raw_image_dataset_resource.rb

@@ -1,5 +1,3 @@
-require 'active_resource'
-
 class RawImageDatasetResource < ActiveResource::Base
   self.site = VisitRawDataDirectory::DATAPANDA_SERVER
   self.element_name = "image_dataset"

data/lib/metamri/visit_raw_data_directory.rb

@@ -6,6 +6,7 @@ require 'tmpdir'
 require 'fileutils'
 require 'sqlite3'
 require 'logger'
+require 'pp'
 require 'metamri/raw_image_file'
 require 'metamri/raw_image_dataset'
 
@@ -81,11 +82,20 @@ class VisitRawDataDirectory
   # pfiles are scanned and imported in addition to one and only one dicom file.  After scanning
   # @datasets will hold an array of ImageDataset instances.  Setting the rmr here can raise an 
   # exception if no valid rmr is found in the datasets, be prepared to catch it.
-  def scan
+  #
+  # Run a scan with the following options:
+  # - :ignore_patterns - An array of Regular Expressions that will be used to skip heavy directories.
+  def scan(options = {})
     flash "Scanning visit raw data directory #{@visit_directory}" if $LOG.level <= Logger::INFO
+    default_options = {:ignore_patterns => []}
+    options = default_options.merge(options)
+    puts "Ignoring directories matching: #{options[:ignore_patterns].join(", ")}" unless options[:ignore_patterns].empty?
+    
     d = Pathname.new(@visit_directory)
     d.each_subdirectory do |dd|
-      begin 
+      begin
+        matches = options[:ignore_patterns].collect {|pat| dd.to_s =~ pat ? dd : nil }.compact
+        next unless matches.empty?
         dd.each_pfile { |pf| @datasets << import_dataset(pf, dd) }
         dd.first_dicom { |fd| @datasets << import_dataset(fd, dd) }
       rescue Exception => e

data/lib/metamri/visit_raw_data_directory_resource.rb

@@ -1,6 +1,4 @@
 $:.unshift File.dirname(__FILE__)
-
-require 'active_resource'
 require 'raw_image_dataset_resource'
 
 class VisitRawDataDirectoryResource < ActiveResource::Base

data/lib/metamri.rb

@@ -1,5 +1,12 @@
 $: << File.dirname(__FILE__)
 
+begin
+  require 'rubygems'
+  gem 'activeresource', '<= 2.3.8'
+  require 'active_resource'
+end
+
+
 require 'metamri/core_additions'
 require 'metamri/raw_image_file'
 require 'metamri/raw_image_dataset'

data/metamri.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{metamri}
-  s.version = "0.1.18"
+  s.version = "0.1.19"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Kristopher J. Kosmatka"]
-  s.date = %q{2010-06-04}
+  s.date = %q{2010-07-09}
   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{1.3.6}
+  s.rubygems_version = %q{1.3.7}
   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::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
+    if Gem::Version.new(Gem::VERSION) >= 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

@@ -1,12 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: metamri
 version: !ruby/object:Gem::Version 
+  hash: 61
   prerelease: false
   segments: 
   - 0
   - 1
-  - 18
-  version: 0.1.18
+  - 19
+  version: 0.1.19
 platform: ruby
 authors: 
 - Kristopher J. Kosmatka
@@ -14,16 +15,18 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-06-04 00:00:00 -05:00
+date: 2010-07-09 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"
@@ -33,9 +36,11 @@ dependencies:
   name: dicom
   prerelease: false
   requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
+        hash: 3
         segments: 
         - 0
         version: "0"
@@ -45,9 +50,11 @@ dependencies:
   name: rspec
   prerelease: false
   requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
+        hash: 3
         segments: 
         - 0
         version: "0"
@@ -105,23 +112,27 @@ 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: 1.3.6
+rubygems_version: 1.3.7
 signing_key: 
 specification_version: 3
 summary: MRI metadata