metamri 0.2.5 → 0.2.6

data/Gemfile

@@ -0,0 +1,7 @@
+source "http://rubygems.org"
+
+# Specify your gem's dependencies in metamri.gemspec
+gemspec
+
+gem 'activeresource', '~>3.0', :require => 'active_resource'
+gem 'hirb', '~>0.4'

data/Gemfile.lock

@@ -0,0 +1,43 @@
+PATH
+  remote: .
+  specs:
+    metamri (0.2.5)
+      activeresource (~> 3.0)
+      dicom (~> 0.8)
+      metamri
+      sqlite3 (~> 1.3.3)
+
+GEM
+  remote: http://rubygems.org/
+  specs:
+    activemodel (3.0.9)
+      activesupport (= 3.0.9)
+      builder (~> 2.1.2)
+      i18n (~> 0.5.0)
+    activeresource (3.0.9)
+      activemodel (= 3.0.9)
+      activesupport (= 3.0.9)
+    activesupport (3.0.9)
+    builder (2.1.2)
+    dicom (0.9.1)
+    diff-lcs (1.1.2)
+    hirb (0.4.5)
+    i18n (0.5.0)
+    rspec (2.6.0)
+      rspec-core (~> 2.6.0)
+      rspec-expectations (~> 2.6.0)
+      rspec-mocks (~> 2.6.0)
+    rspec-core (2.6.4)
+    rspec-expectations (2.6.0)
+      diff-lcs (~> 1.1.2)
+    rspec-mocks (2.6.0)
+    sqlite3 (1.3.3)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  activeresource (~> 3.0)
+  hirb (~> 0.4)
+  metamri!
+  rspec (~> 2.5)

data/Rakefile

@@ -1,6 +1,6 @@
 require 'rubygems'
 require 'rake'
-require 'rake/rdoctask'
+require 'rdoc/task'
 require 'rake/testtask'
 
 begin
@@ -11,11 +11,12 @@ begin
     gemspec.description = "Extraction of MRI metadata and insertion into compatible sqlite3 databases."
     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_dependency('dicom')
-    # gemspec.add_dependency('rmagick')
-    gemspec.add_development_dependency('rspec')
+    gemspec.authors = ["Kristopher J. Kosmatka", "Erik Kastman"]
+    gemspec.add_dependency('sqlite3', '~>1.3.3')
+    gemspec.add_dependency('dicom', '~>0.8')
+    gemspec.add_dependency('activeresource', '~>3.0')
+    gemspec.add_development_dependency('rspec', '~>2.5')
+
   end
   Jeweler::GemcutterTasks.new
 rescue LoadError

data/VERSION

@@ -1 +1 @@
-0.2.5
+0.2.6

data/bin/list_visit

@@ -55,6 +55,7 @@ def run!
         list_visit raw_directory, options
       rescue StandardError => e
         puts e
+        puts e.backtrace if $LOG.level <= Logger::DEBUG
         next
       end
     end

data/lib/metamri/core_additions.rb

@@ -46,7 +46,12 @@ class Pathname
         begin
           yield lc
         rescue StandardError => e
-          puts "#{e}"
+          case $LOG.level
+          when Logger::DEBUG
+            raise e
+          else
+            puts "#{e}"
+          end
         ensure
           lc.delete
         end

data/lib/metamri/raw_image_dataset_thumbnail.rb

@@ -1,7 +1,7 @@
 require 'tmpdir'
 begin
   %W{dicom RMagick}.each do |lib|
-    require lib
+    require lib unless defined?(lib)
   end
 rescue LoadError => e
   raise LoadError, "Could not load #{e}.  Thumbnailing will use slicer instead of ruby-dicom."

data/lib/metamri/raw_image_file.rb

@@ -107,12 +107,13 @@ class RawImageFile
     # file type is based on file name but only if the header was read successfully
     @file_type = determine_file_type
     
-    # try to import attributes from the header, raise an ioerror if any attributes
-    # are not found
+    # try to import attributes from the header, raise an ScriptError or NoMethodError 
+    # if any required attributes are not found
     begin
       import_hdr
     rescue ScriptError, NoMethodError => e
-      raise IOError, "Could not find required DICOM Header Meta Element: #{e}"
+      # puts e.backtrace
+      raise e, "Could not find required DICOM Header Meta Element: #{e}"
     rescue StandardError => e
       raise e, "Header import failed for file #{@filename}.  #{e}"
     end
@@ -619,7 +620,7 @@ private
     @rep_time = ($1).to_f / 1000000
     
     study_uid_pat =~ @hdr_data
-    @dicom_study_uid = ($1).strip.chomp
+    @dicom_study_uid = ($1).strip.chomp unless $1.nil?
     
     series_uid_pat =~ @hdr_data
     @dicom_series_uid = ($1).strip.chomp

data/lib/metamri/visit_raw_data_directory.rb

@@ -59,9 +59,9 @@ class VisitRawDataDirectory
   # DICOM Study UID (Visit/Study Unique Identifier)
   attr_reader :dicom_study_uid
   
-  PREPROCESS_REPOSITORY_DIRECTORY = '/Data/vtrak1/preprocessed/visits'
-  # DATAPANDA_SERVER = 'http://localhost:3000'
-  DATAPANDA_SERVER = 'http://nelson'
+  PREPROCESS_REPOSITORY_DIRECTORY = '/Data/vtrak1/preprocessed/visits' unless defined?(PREPROCESS_REPOSITORY_DIRECTORY)
+  DATAPANDA_SERVER = 'http://nelson' unless defined?(DATAPANDA_SERVER)
+  # DATAPANDA_SERVER = 'http://localhost:3000' unless defined?(DATAPANDA_SERVER)
 
   
   # A new Visit instance needs to know the path to its raw data and scan_procedure name.  The scan_procedure
@@ -342,8 +342,9 @@ Returns an array of the created nifti files.
     
     begin
       rawimagefile = RawImageFile.new(rawfile.to_s)
-    # rescue Exception => e
-    #   raise(e, "+++ Trouble reading raw image file #{rawfile}. #{e}")
+    # rescue StandardError => e
+      # puts e.backtrace
+      # raise(e, "+++ Trouble reading raw image file #{rawfile}. #{e}")
     end
     
     return RawImageDataset.new(original_parent_directory.to_s, [rawimagefile])

data/lib/metamri/visit_raw_data_directory_resource.rb

@@ -19,7 +19,7 @@ class VisitRawDataDirectoryResource < ActiveResource::Base
   end
   
   def datasets
-    @datasets ||= RawImageDatasetResource.find(:all, :from => "/visits/#{id}/image_datasets.xml" )
+    @datasets ||= RawImageDatasetResource.find(:all, :from => RawImageDatasetResource.collection_path('search[visit_id_eq]' => "#{id}"))
   end
   
   # Convert a Resource and its datasets to a VisitRawDataDirectory and 

data/lib/metamri.rb

@@ -1,10 +1,13 @@
 $: << File.dirname(__FILE__)
 
-# begin
-#   require 'rubygems'
-#   gem 'activeresource', '<= 2.3.8'
-  require 'active_resource'
-# end
+
+begin
+  require 'rubygems'
+  require "bundler/setup"
+  Bundler.require(:default)
+  
+rescue LoadError
+end
 
 
 require 'metamri/core_additions'

data/metamri.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{metamri}
-  s.version = "0.2.5"
+  s.version = "0.2.6"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.authors = ["Kristopher J. Kosmatka"]
-  s.date = %q{2011-03-14}
+  s.authors = ["Kristopher J. Kosmatka", "Erik Kastman"]
+  s.date = %q{2011-07-26}
   s.description = %q{Extraction of MRI metadata and insertion into compatible sqlite3 databases.}
   s.email = %q{kk4@medicine.wisc.edu}
   s.executables = ["convert_visit.rb", "import_visit.rb", "import_respiratory_files.rb", "import_study.rb", "list_visit"]
@@ -18,6 +18,8 @@ Gem::Specification.new do |s|
   ]
   s.files = [
     ".rspec",
+    "Gemfile",
+    "Gemfile.lock",
     "Manifest",
     "README.rdoc",
     "Rakefile",
@@ -80,18 +82,39 @@ Gem::Specification.new do |s|
     s.specification_version = 3
 
     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"])
+      s.add_runtime_dependency(%q<metamri>, [">= 0"])
+      s.add_runtime_dependency(%q<activeresource>, ["~> 3.0"])
+      s.add_runtime_dependency(%q<hirb>, ["~> 0.4"])
+      s.add_development_dependency(%q<rspec>, ["~> 2.5"])
+      s.add_development_dependency(%q<rspec>, ["~> 2.5"])
+      s.add_development_dependency(%q<rspec>, ["~> 2.5"])
+      s.add_runtime_dependency(%q<sqlite3>, ["~> 1.3.3"])
+      s.add_runtime_dependency(%q<dicom>, ["~> 0.8"])
+      s.add_runtime_dependency(%q<activeresource>, ["~> 3.0"])
+      s.add_development_dependency(%q<rspec>, ["~> 2.5"])
     else
-      s.add_dependency(%q<sqlite3-ruby>, [">= 0"])
-      s.add_dependency(%q<dicom>, [">= 0"])
-      s.add_dependency(%q<rspec>, [">= 0"])
+      s.add_dependency(%q<metamri>, [">= 0"])
+      s.add_dependency(%q<activeresource>, ["~> 3.0"])
+      s.add_dependency(%q<hirb>, ["~> 0.4"])
+      s.add_dependency(%q<rspec>, ["~> 2.5"])
+      s.add_dependency(%q<rspec>, ["~> 2.5"])
+      s.add_dependency(%q<rspec>, ["~> 2.5"])
+      s.add_dependency(%q<sqlite3>, ["~> 1.3.3"])
+      s.add_dependency(%q<dicom>, ["~> 0.8"])
+      s.add_dependency(%q<activeresource>, ["~> 3.0"])
+      s.add_dependency(%q<rspec>, ["~> 2.5"])
     end
   else
-    s.add_dependency(%q<sqlite3-ruby>, [">= 0"])
-    s.add_dependency(%q<dicom>, [">= 0"])
-    s.add_dependency(%q<rspec>, [">= 0"])
+    s.add_dependency(%q<metamri>, [">= 0"])
+    s.add_dependency(%q<activeresource>, ["~> 3.0"])
+    s.add_dependency(%q<hirb>, ["~> 0.4"])
+    s.add_dependency(%q<rspec>, ["~> 2.5"])
+    s.add_dependency(%q<rspec>, ["~> 2.5"])
+    s.add_dependency(%q<rspec>, ["~> 2.5"])
+    s.add_dependency(%q<sqlite3>, ["~> 1.3.3"])
+    s.add_dependency(%q<dicom>, ["~> 0.8"])
+    s.add_dependency(%q<activeresource>, ["~> 3.0"])
+    s.add_dependency(%q<rspec>, ["~> 2.5"])
   end
 end
 

metadata

@@ -1,27 +1,29 @@
 --- !ruby/object:Gem::Specification 
 name: metamri
 version: !ruby/object:Gem::Version 
-  hash: 29
+  hash: 27
   prerelease: 
   segments: 
   - 0
   - 2
-  - 5
-  version: 0.2.5
+  - 6
+  version: 0.2.6
 platform: ruby
 authors: 
 - Kristopher J. Kosmatka
+- Erik Kastman
 autorequire: 
 bindir: bin
 cert_chain: []
 
-date: 2011-03-14 00:00:00 -05:00
+date: 2011-07-26 00:00:00 -05:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
-  name: sqlite3-ruby
   prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
+  name: metamri
+  type: :runtime
+  version_requirements: &id001 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -30,36 +32,143 @@ dependencies:
         segments: 
         - 0
         version: "0"
+  requirement: *id001
+- !ruby/object:Gem::Dependency 
+  prerelease: false
+  name: activeresource
   type: :runtime
-  version_requirements: *id001
+  version_requirements: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 7
+        segments: 
+        - 3
+        - 0
+        version: "3.0"
+  requirement: *id002
 - !ruby/object:Gem::Dependency 
-  name: dicom
   prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  name: hirb
+  type: :runtime
+  version_requirements: &id003 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
-    - - ">="
+    - - ~>
       - !ruby/object:Gem::Version 
         hash: 3
         segments: 
         - 0
-        version: "0"
-  type: :runtime
-  version_requirements: *id002
+        - 4
+        version: "0.4"
+  requirement: *id003
+- !ruby/object:Gem::Dependency 
+  prerelease: false
+  name: rspec
+  type: :development
+  version_requirements: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 9
+        segments: 
+        - 2
+        - 5
+        version: "2.5"
+  requirement: *id004
 - !ruby/object:Gem::Dependency 
+  prerelease: false
   name: rspec
+  type: :development
+  version_requirements: &id005 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 9
+        segments: 
+        - 2
+        - 5
+        version: "2.5"
+  requirement: *id005
+- !ruby/object:Gem::Dependency 
   prerelease: false
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  name: rspec
+  type: :development
+  version_requirements: &id006 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
-    - - ">="
+    - - ~>
       - !ruby/object:Gem::Version 
-        hash: 3
+        hash: 9
+        segments: 
+        - 2
+        - 5
+        version: "2.5"
+  requirement: *id006
+- !ruby/object:Gem::Dependency 
+  prerelease: false
+  name: sqlite3
+  type: :runtime
+  version_requirements: &id007 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 29
+        segments: 
+        - 1
+        - 3
+        - 3
+        version: 1.3.3
+  requirement: *id007
+- !ruby/object:Gem::Dependency 
+  prerelease: false
+  name: dicom
+  type: :runtime
+  version_requirements: &id008 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 27
         segments: 
         - 0
-        version: "0"
+        - 8
+        version: "0.8"
+  requirement: *id008
+- !ruby/object:Gem::Dependency 
+  prerelease: false
+  name: activeresource
+  type: :runtime
+  version_requirements: &id009 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 7
+        segments: 
+        - 3
+        - 0
+        version: "3.0"
+  requirement: *id009
+- !ruby/object:Gem::Dependency 
+  prerelease: false
+  name: rspec
   type: :development
-  version_requirements: *id003
+  version_requirements: &id010 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 9
+        segments: 
+        - 2
+        - 5
+        version: "2.5"
+  requirement: *id010
 description: Extraction of MRI metadata and insertion into compatible sqlite3 databases.
 email: kk4@medicine.wisc.edu
 executables: 
@@ -74,6 +183,8 @@ extra_rdoc_files:
 - README.rdoc
 files: 
 - .rspec
+- Gemfile
+- Gemfile.lock
 - Manifest
 - README.rdoc
 - Rakefile