metamri 0.1.11 → 0.1.13
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- data/Rakefile +2 -0
- data/VERSION +1 -1
- data/bin/list_visit +30 -15
- data/lib/metamri/raw_image_dataset_resource.rb +13 -1
- data/lib/metamri/visit_raw_data_directory_resource.rb +15 -3
- data/metamri.gemspec +8 -2
- metadata +23 -4
data/Rakefile
CHANGED
@@ -27,6 +27,8 @@ begin
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|
27
27
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gemspec.email = "kk4@medicine.wisc.edu"
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28
28
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gemspec.homepage = "http://github.com/brainmap/metamri"
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29
29
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gemspec.authors = ["Kristopher J. Kosmatka"]
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30
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+
gemspec.add_dependency('sqlite3-ruby')
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31
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+
gemspec.add_development_dependency('rspec')
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30
32
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end
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31
33
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Jeweler::GemcutterTasks.new
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32
34
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rescue LoadError
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data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
0.1.
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1
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+
0.1.13
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data/bin/list_visit
CHANGED
@@ -35,26 +35,40 @@ $:.unshift File.join(File.dirname(__FILE__),'..','lib')
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35
35
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require 'metamri'
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36
36
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require 'pathname'
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37
37
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require 'rdoc/usage'
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38
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-
require 'logger'
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38
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+
# require 'logger'
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39
39
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40
40
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def list_visit(raw_directory)
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41
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-
$LOG = Logger.new(STDOUT)
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42
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-
$LOG.level = Logger::INFO
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43
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-
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44
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-
#
|
45
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-
|
41
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+
# $LOG = Logger.new(STDOUT)
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42
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+
# $LOG.level = Logger::INFO
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43
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+
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44
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+
# First try to lookup Visit and Datasets through active_resource
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45
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+
# Then fall back to scanning them fresh.
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46
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+
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46
47
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begin
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47
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-
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48
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-
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49
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-
|
50
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-
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51
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-
raise e
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48
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+
# raise
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49
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+
visit = VisitRawDataDirectoryResource.find(:first, :params => {:search => {:path => raw_directory}})
|
50
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+
raise "Could not lookup visit using path." unless visit
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51
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+
raise "Incorrect visit found." unless visit.path == raw_directory
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52
52
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rescue Exception => e
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53
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-
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54
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-
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55
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-
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53
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+
puts e
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54
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+
visit = VisitRawDataDirectory.new(raw_directory)
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55
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+
begin
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56
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+
visit.scan
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57
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+
rescue IndexError => e
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58
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+
$LOG.error "Are you sure #{raw_directory} is a valid raw visit directory?"
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59
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+
raise e
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60
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+
end
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56
61
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end
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62
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+
|
63
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+
# begin
|
64
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+
# rescue Exception => e
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65
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+
# $LOG.error "There was a problem scanning a dataset in #{visit.visit_directory}... skipping."
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66
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+
# $LOG.error "Exception message: #{e.message}"
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67
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+
# raise e
|
68
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+
# end
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57
69
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|
70
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+
# Visit is Either a RawVisitDataDirectory or a RawVisitDataDirectoryResource
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71
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+
# Either can handle printing to_s
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58
72
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visit.to_s
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59
73
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60
74
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end
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@@ -63,7 +77,8 @@ if File.basename(__FILE__) == File.basename($PROGRAM_NAME)
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63
77
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RDoc::usage() if (ARGV[0] == '-h')
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64
78
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|
65
79
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# Default to scanning the current directory if no argument was given.
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66
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-
raw_directory = ARGV[0] ||=
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80
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+
raw_directory = ARGV[0] ||= Dir.pwd
|
81
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+
raw_directory = File.expand_path(raw_directory)
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67
82
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|
68
83
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list_visit(raw_directory)
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69
84
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end
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@@ -7,7 +7,7 @@ class RawImageDatasetResource < ActiveResource::Base
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7
7
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# Creates a Backwards Transfer to go from ActiveRecord to Metamri Classes
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8
8
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# ActiveResource will provide :attr methods for column names from the database,
|
9
9
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# so check the current schema.rb file for those.
|
10
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-
def
|
10
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+
def to_metamri_raw_image_dataset
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11
11
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# A Metamri Class requires at least one valid image file.
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12
12
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# This is a little tricky since we really only care about the variables, not rescanning them.
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13
13
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@@ -17,4 +17,16 @@ class RawImageDatasetResource < ActiveResource::Base
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17
17
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|
18
18
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return @dataset
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19
19
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end
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20
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+
|
21
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+
# Map RawImageDatasetResource and RawImageDataset
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22
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+
# def method_missing(m, *args, &block)
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23
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+
# puts m
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24
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+
# if m == :directory
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25
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+
# path
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26
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+
# elsif m == :directory_basename
|
27
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+
# File.basename(directory)
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28
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+
# else
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29
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+
# super
|
30
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+
# end
|
31
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+
# end
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20
32
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end
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@@ -1,6 +1,7 @@
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1
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-
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1
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+
$:.unshift File.dirname(__FILE__)
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2
2
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|
3
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-
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3
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+
require 'active_resource'
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4
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+
require 'raw_image_dataset_resource'
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4
5
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|
5
6
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class VisitRawDataDirectoryResource < ActiveResource::Base
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6
7
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self.site = VisitRawDataDirectory::DATAPANDA_SERVER
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@@ -17,4 +18,15 @@ class VisitRawDataDirectoryResource < ActiveResource::Base
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17
18
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@visit.database_id = id
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18
19
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return @visit
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19
20
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end
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20
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-
|
21
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+
|
22
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+
def datasets
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23
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+
@datasets ||= RawImageDatasetResource.find(:all, :from => "/visits/#{id}/image_datasets.xml" )
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24
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+
end
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25
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+
|
26
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+
def to_s
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27
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+
metamri_visit = to_metamri_visit_raw_data_directory
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28
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+
metamri_visit.datasets = datasets.collect { |ds| ds.to_metamri_raw_image_dataset}
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29
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+
metamri_visit.to_s
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30
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+
end
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31
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+
end
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32
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+
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data/metamri.gemspec
CHANGED
@@ -5,11 +5,11 @@
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5
5
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6
6
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Gem::Specification.new do |s|
|
7
7
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s.name = %q{metamri}
|
8
|
-
s.version = "0.1.
|
8
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+
s.version = "0.1.13"
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9
9
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|
10
10
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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11
11
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s.authors = ["Kristopher J. Kosmatka"]
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12
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-
s.date = %q{2010-02-
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12
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+
s.date = %q{2010-02-04}
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13
13
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s.description = %q{Extraction of MRI metadata and insertion into compatible sqlite3 databases.}
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14
14
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s.email = %q{kk4@medicine.wisc.edu}
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15
15
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s.executables = ["import_study.rb", "import_visit.rb", "import_respiratory_files.rb", "list_visit", "convert_visit.rb"]
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@@ -63,9 +63,15 @@ Gem::Specification.new do |s|
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63
63
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s.specification_version = 3
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64
64
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|
65
65
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if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
|
66
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+
s.add_runtime_dependency(%q<sqlite3-ruby>, [">= 0"])
|
67
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+
s.add_development_dependency(%q<rspec>, [">= 0"])
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66
68
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else
|
69
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+
s.add_dependency(%q<sqlite3-ruby>, [">= 0"])
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70
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+
s.add_dependency(%q<rspec>, [">= 0"])
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67
71
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end
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68
72
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else
|
73
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+
s.add_dependency(%q<sqlite3-ruby>, [">= 0"])
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74
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+
s.add_dependency(%q<rspec>, [">= 0"])
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69
75
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end
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70
76
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end
|
71
77
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|
metadata
CHANGED
@@ -1,7 +1,7 @@
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|
1
1
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--- !ruby/object:Gem::Specification
|
2
2
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name: metamri
|
3
3
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version: !ruby/object:Gem::Version
|
4
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-
version: 0.1.
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4
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+
version: 0.1.13
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5
5
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platform: ruby
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6
6
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authors:
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7
7
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- Kristopher J. Kosmatka
|
@@ -9,10 +9,29 @@ autorequire:
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|
9
9
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bindir: bin
|
10
10
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cert_chain: []
|
11
11
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|
12
|
-
date: 2010-02-
|
12
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+
date: 2010-02-04 00:00:00 -06:00
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13
13
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default_executable:
|
14
|
-
dependencies:
|
15
|
-
|
14
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+
dependencies:
|
15
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+
- !ruby/object:Gem::Dependency
|
16
|
+
name: sqlite3-ruby
|
17
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+
type: :runtime
|
18
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+
version_requirement:
|
19
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+
version_requirements: !ruby/object:Gem::Requirement
|
20
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+
requirements:
|
21
|
+
- - ">="
|
22
|
+
- !ruby/object:Gem::Version
|
23
|
+
version: "0"
|
24
|
+
version:
|
25
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+
- !ruby/object:Gem::Dependency
|
26
|
+
name: rspec
|
27
|
+
type: :development
|
28
|
+
version_requirement:
|
29
|
+
version_requirements: !ruby/object:Gem::Requirement
|
30
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+
requirements:
|
31
|
+
- - ">="
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32
|
+
- !ruby/object:Gem::Version
|
33
|
+
version: "0"
|
34
|
+
version:
|
16
35
|
description: Extraction of MRI metadata and insertion into compatible sqlite3 databases.
|
17
36
|
email: kk4@medicine.wisc.edu
|
18
37
|
executables:
|