diff options
| -rw-r--r-- | Rakefile | 2 | ||||
| -rw-r--r-- | VERSION | 2 | ||||
| -rw-r--r-- | lib/algorithm.rb | 7 | ||||
| -rw-r--r-- | lib/r-util.rb | 123 | ||||
| -rw-r--r-- | lib/stratification.R | 78 | ||||
| -rw-r--r-- | lib/transform.rb | 4 | ||||
| -rw-r--r-- | opentox-ruby.gemspec | 200 |
7 files changed, 268 insertions, 148 deletions
@@ -42,7 +42,7 @@ begin gem.add_dependency "dm-migrations", "=1.1.0" gem.add_dependency "dm-validations", "=1.1.0" gem.add_dependency "dm-sqlite-adapter", "=1.1.0" - gem.add_dependency "ruby-plot", "=0.6.0" + gem.add_dependency "ruby-plot", "=0.6.1" gem.add_dependency "gsl", "=1.14.7" gem.add_dependency "statsample", "=1.1.0" @@ -1 +1 @@ -3.1.0
\ No newline at end of file +3.1.0 diff --git a/lib/algorithm.rb b/lib/algorithm.rb index c026c56..9dcf6a8 100644 --- a/lib/algorithm.rb +++ b/lib/algorithm.rb @@ -381,10 +381,10 @@ module OpenTox else #LOGGER.debug gram_matrix.to_yaml @r = RinRuby.new(false,false) # global R instance leads to Socket errors after a large number of requests - @r.eval "set.seed(1)" @r.eval "suppressPackageStartupMessages(library('caret'))" # requires R packages "caret" and "kernlab" @r.eval "suppressPackageStartupMessages(library('doMC'))" # requires R packages "multicore" @r.eval "registerDoMC()" # switch on parallel processing + @r.eval "set.seed(1)" begin # set data @@ -417,7 +417,7 @@ module OpenTox # model + support vectors LOGGER.debug "Creating R SVM model ..." - @r.eval <<-EOR + train_success = @r.eval <<-EOR model = train(prop_matrix,y,method="svmradial",tuneLength=8,trControl=trainControl(method="LGOCV",number=10),preProcess=c("center", "scale")) perf = ifelse ( class(y)!='numeric', max(model$results$Accuracy), model$results[which.min(model$results$RMSE),]$Rsquared ) EOR @@ -431,6 +431,7 @@ module OpenTox # censoring prediction = nil if ( @r.perf.nan? || @r.perf < min_train_performance ) + prediction = nil unless train_success LOGGER.debug "Performance: #{sprintf("%.2f", @r.perf)}" rescue Exception => e LOGGER.debug "#{e.class}: #{e.message}" @@ -459,12 +460,12 @@ module OpenTox # need packs 'randomForest', 'RANN' @r.eval <<-EOR - set.seed(1) suppressPackageStartupMessages(library('caret')) suppressPackageStartupMessages(library('randomForest')) suppressPackageStartupMessages(library('RANN')) suppressPackageStartupMessages(library('doMC')) registerDoMC() + set.seed(1) acts = read.csv(ds_csv_file, check.names=F) feats = read.csv(fds_csv_file, check.names=F) diff --git a/lib/r-util.rb b/lib/r-util.rb index 7163c46..0d4e82c 100644 --- a/lib/r-util.rb +++ b/lib/r-util.rb @@ -8,6 +8,18 @@ PACKAGE_DIR = package_dir require "tempfile" +class Array + + def check_uniq + hash = {} + self.each do |x| + raise "duplicate #{x}" if hash[x] + hash[x] = true + end + end + +end + module OpenTox class RUtil @@ -75,12 +87,10 @@ module OpenTox end # embedds feature values of two datasets into 2D and plots it - # fast_plot = true -> PCA, fast_plot = false -> SMACOF (iterative optimisation method) # def feature_value_plot(files, dataset_uri1, dataset_uri2, dataset_name1, dataset_name2, - features=nil, fast_plot=true, subjectid=nil, waiting_task=nil) + features=nil, subjectid=nil, waiting_task=nil) - raise "r-package smacof missing" if fast_plot==false and !package_installed?("smacof") LOGGER.debug("r-util> create feature value plot") d1 = OpenTox::Dataset.find(dataset_uri1,subjectid) d2 = OpenTox::Dataset.find(dataset_uri2,subjectid) @@ -102,17 +112,13 @@ module OpenTox @r.eval "split <- c(rep(0,nrow(#{df1})),rep(1,nrow(#{df2})))" @r.names = [dataset_name1, dataset_name2] LOGGER.debug("r-util> - convert data to 2d") - @r.eval "df.2d <- plot_pre_process(df, method='#{(fast_plot ? "pca" : "smacof")}')" + #@r.eval "save.image(\"/tmp/image.R\")" + @r.eval "df.2d <- plot_pre_process(df, method='sammon')" waiting_task.progress(75) if waiting_task - if fast_plot - info = "main='PCA-Embedding of #{features.size} features',xlab='PC1',ylab='PC2'" - else - info = "main='SMACOF-Embedding of #{features.size} features',xlab='x',ylab='y'" - end LOGGER.debug("r-util> - plot data") plot_to_files(files) do |file| - @r.eval "plot_split( df.2d, split, names, #{info})" + @r.eval "plot_split( df.2d, split, names, main='Sammon embedding of #{features.size} features',xlab='x',ylab='y')" end end @@ -170,19 +176,68 @@ module OpenTox end end - # stratified splits a dataset into two dataset the feature values + # stratified splits a dataset into two dataset according to the feature values + # all features are taken into account unless <split_features> is given + # returns two datases + def stratified_split( dataset, metadata={}, missing_values="NA", pct=0.3, subjectid=nil, seed=42, split_features=nil ) + stratified_split_internal( dataset, metadata, missing_values, nil, pct, subjectid, seed, split_features ) + end + + # stratified splits a dataset into k datasets according the feature values # all features are taken into account unless <split_features> is given - def stratified_split( dataset, missing_values="NA", pct=0.3, subjectid=nil, seed=42, split_features=nil ) + # returns two arrays of datasets + def stratified_k_fold_split( dataset, metadata={}, missing_values="NA", num_folds=10, subjectid=nil, seed=42, split_features=nil ) + stratified_split_internal( dataset, metadata, missing_values, num_folds, nil, subjectid, seed, split_features ) + end + + private + def stratified_split_internal( dataset, metadata={}, missing_values="NA", num_folds=nil, pct=nil, subjectid=nil, seed=42, split_features=nil ) + raise "internal error" if num_folds!=nil and pct!=nil + k_fold_split = num_folds!=nil + if k_fold_split + raise "num_folds not a fixnum: #{num_folds}" unless num_folds.is_a?(Fixnum) + else + raise "pct is not a numeric: #{pct}" unless pct.is_a?(Numeric) + end raise "not a loaded ot-dataset" unless dataset.is_a?(OpenTox::Dataset) and dataset.compounds.size>0 and dataset.features.size>0 + raise "missing_values=#{missing_values}" unless missing_values.is_a?(String) or missing_values==0 + raise "subjectid=#{subjectid}" unless subjectid==nil or subjectid.is_a?(String) LOGGER.debug("r-util> apply stratified split to #{dataset.uri}") - df = dataset_to_dataframe( dataset, missing_values, subjectid, split_features ) + df = dataset_to_dataframe( dataset, missing_values, subjectid) @r.eval "set.seed(#{seed})" - @r.eval "split <- stratified_split(#{df}, ratio=#{pct})" - split = @r.pull 'split' - split = split.collect{|s| 1-s.to_i} # reverse 1s and 0s, as 1 means selected, but 0 will be first set - split_to_datasets( df, split, subjectid ) + str_split_features = "" + if split_features + @r.split_features = split_features if split_features + str_split_features = "colnames=split_features" + end + @r.eval "save.image(\"/tmp/image.R\")" + + if k_fold_split + @r.eval "split <- stratified_k_fold_split(#{df}, num_folds=#{num_folds}, #{str_split_features})" + split = @r.pull 'split' + train = [] + test = [] + num_folds.times do |f| + datasetname = 'dataset fold '+(f+1).to_s+' of '+num_folds.to_s + metadata[DC.title] = "training "+datasetname + train << split_to_dataset( df, split, metadata, subjectid ){ |i| i!=(f+1) } + metadata[DC.title] = "test "+datasetname + test << split_to_dataset( df, split, metadata, subjectid ){ |i| i==(f+1) } + end + return train, test + else + puts "split <- stratified_split(#{df}, ratio=#{pct}, #{str_split_features})" + @r.eval "split <- stratified_split(#{df}, ratio=#{pct}, #{str_split_features})" + split = @r.pull 'split' + metadata[DC.title] = "Training dataset split of "+dataset.uri + train = split_to_dataset( df, split, metadata, subjectid ){ |i| i==1 } + metadata[DC.title] = "Test dataset split of "+dataset.uri + test = split_to_dataset( df, split, metadata, subjectid ){ |i| i==0 } + return train, test + end end + public # dataset should be loaded completely (use Dataset.find) # takes duplicates into account @@ -212,9 +267,13 @@ module OpenTox features = dataset.features.keys.sort end compounds = [] + compound_names = [] dataset.compounds.each do |c| + count = 0 num_compounds[c].times do |i| compounds << c + compound_names << "#{c}$#{count}" + count+=1 end end @@ -238,7 +297,7 @@ module OpenTox end end df_name = "df_#{dataset.uri.split("/")[-1].split("?")[0]}" - assign_dataframe(df_name,d_values,compounds,features) + assign_dataframe(df_name,d_values,compound_names,features) # set dataframe column types accordingly f_count = 1 #R starts at 1 @@ -264,16 +323,18 @@ module OpenTox # converts a dataframe into a dataset (a new dataset is created at the dataset webservice) # this is only possible if a superset of the dataframe was created by dataset_to_dataframe (metadata and URIs!) - def dataframe_to_dataset( df, subjectid=nil ) - dataframe_to_dataset_indices( df, subjectid, nil) + def dataframe_to_dataset( df, metadata={}, subjectid=nil ) + dataframe_to_dataset_indices( df, metadata, subjectid, nil) end private - def dataframe_to_dataset_indices( df, subjectid=nil, compound_indices=nil ) + def dataframe_to_dataset_indices( df, metadata={}, subjectid=nil, compound_indices=nil ) raise unless @@feats[df].size>0 - values, compounds, features = pull_dataframe(df) + values, compound_names, features = pull_dataframe(df) + compounds = compound_names.collect{|c| c.split("$")[0]} features.each{|f| raise unless @@feats[df][f]} dataset = OpenTox::Dataset.create(CONFIG[:services]["opentox-dataset"],subjectid) + dataset.add_metadata(metadata) LOGGER.debug "r-util> convert dataframe to dataset #{dataset.uri}" compounds.size.times{|i| dataset.add_compound(compounds[i]) if compound_indices==nil or compound_indices.include?(i)} features.each{|f| dataset.add_feature(f,@@feats[df][f])} @@ -290,16 +351,12 @@ module OpenTox dataset end - def split_to_datasets( df, split, subjectid=nil ) - sets = [] - (split.min.to_i .. split.max.to_i).each do |i| - indices = [] - split.size.times{|j| indices<<j if split[j]==i} - dataset = dataframe_to_dataset_indices( df, subjectid, indices ) - LOGGER.debug("r-util> split into #{dataset.uri}, c:#{dataset.compounds.size}, f:#{dataset.features.size}") - sets << dataset - end - sets + def split_to_dataset( df, split, metadata={}, subjectid=nil ) + indices = [] + split.size.times{|i| indices<<i if yield(split[i]) } + dataset = dataframe_to_dataset_indices( df, metadata, subjectid, indices ) + LOGGER.debug("r-util> split into #{dataset.uri}, c:#{dataset.compounds.size}, f:#{dataset.features.size}") + dataset end def pull_dataframe(df) @@ -323,6 +380,8 @@ module OpenTox end def assign_dataframe(df,input,rownames,colnames) + rownames.check_uniq if rownames + colnames.check_uniq if colnames tmp = File.join(Dir.tmpdir,Time.new.to_f.to_s+"_"+rand(10000).to_s+".csv") file = File.new(tmp, 'w') input.each{|i| file.puts(i.collect{|e| "\"#{e}\""}.join("#")+"\n")} diff --git a/lib/stratification.R b/lib/stratification.R index 76ff2d8..3f8698c 100644 --- a/lib/stratification.R +++ b/lib/stratification.R @@ -1,4 +1,13 @@ +round_it <- function( x ) +{ + if(isTRUE((x - floor(x))>=0.5)) + ceiling(x) + else + floor(x) +} + + nominal_to_binary <- function( data ) { result = NULL @@ -41,9 +50,13 @@ nominal_to_binary <- function( data ) result } -process_data <- function( data ) +process_data <- function( data, colnames=NULL ) { data.num <- as.data.frame(data) + if (!is.null(colnames)) + { + data.num = subset(data.num, select = colnames) + } if (!is.numeric(data.num)) { data.num = nominal_to_binary(data.num) @@ -72,14 +85,15 @@ cluster <- function( data, min=10, max=15 ) cbind(s$partition[,m]) } -stratified_split <- function( data, ratio=0.3, method="cluster" ) +stratified_split <- function( data, ratio=0.3, method="cluster", colnames=NULL ) { - data.processed = as.matrix(process_data( data )) + data.processed = as.matrix(process_data( data, colnames )) + print(paste("split using #features: ",ncol(data.processed))) if (method == "samplecube") { require("sampling") # adjust ratio to make samplecube return exact number of samples - ratio = round(nrow(data.processed)*ratio)/nrow(data.processed) + ratio = round_it(nrow(data.processed)*ratio)/nrow(data.processed) pik = rep(ratio,times=nrow(data.processed)) data.strat = cbind(pik,data.processed) samplecube(data.strat,pik,order=2,comment=F) @@ -101,10 +115,11 @@ stratified_split <- function( data, ratio=0.3, method="cluster" ) stop("unknown method") } -stratified_k_fold_split <- function( data, num_folds=10, method="cluster" ) +stratified_k_fold_split <- function( data, num_folds=10, method="cluster", colnames=NULL ) { print(paste(num_folds,"-fold-split, data-size",nrow(data))) - data.processed = as.matrix(process_data( data )) + data.processed = as.matrix(process_data( data, colnames )) + print(paste("split using #features: ",ncol(data.processed))) if (method == "samplecube") { folds = rep(0, times=nrow(data)) @@ -133,7 +148,7 @@ stratified_k_fold_split <- function( data, num_folds=10, method="cluster" ) { require("TunePareto") cl = cluster(data.processed) - res = generateCVRuns(cl,ntimes=1,nfold=3) + res = generateCVRuns(cl,ntimes=1,nfold=num_folds) folds = rep(0, times=nrow(data)) for (i in 1:num_folds) for(j in 1:length(res[[1]][[i]])) @@ -144,6 +159,50 @@ stratified_k_fold_split <- function( data, num_folds=10, method="cluster" ) stop("unknown method") } +duplicate_indices <- function( data ) { + indices = 1:nrow(data) + z = data + duplicate_index = anyDuplicated(z) + while(duplicate_index) { + duplicate_to_index = anyDuplicated(z[1:duplicate_index,],fromLast=T) + #print(paste(duplicate_index,'is dupl to',duplicate_to_index)) + indices[duplicate_index] <- duplicate_to_index + z[duplicate_index,] <- paste('123$ยง%',duplicate_index) + duplicate_index = anyDuplicated(z) + } + indices +} + +add_duplicates <- function( data, dup_indices ) { + result = data[1,] + for(i in 2:length(dup_indices)) { + row = data[rownames(data)==dup_indices[i],] + if(length(row)==0) + stop(paste('index ',i,' dup-index ',dup_indices[i],'not found in data')) + result = rbind(result, row) + } + rownames(result)<-NULL + result +} + +sammon_duplicates <- function( data, ... ) { + di <- duplicate_indices(data) + print(di) + u <- unique(data) + print(paste('unique data points',nrow(u),'of',nrow(data))) + if(nrow(u) <= 4) stop("number of unqiue datapoints <= 4") + points_unique <- sammon(dist(u), ...)$points + if (nrow(u)<nrow(data)) + { + points <- add_duplicates(points_unique, di) + points + } + else + { + points_unique + } +} + plot_pre_process <- function( data, method="pca" ) { data.processed = process_data( data ) @@ -158,6 +217,11 @@ plot_pre_process <- function( data, method="pca" ) data.emb <- smacofSym(dist(data.processed, method = "euclidean"), ndim=2, verbose=T) data.emb$conf } + else if (method == "sammon") + { + require("MASS") + sammon_duplicates(data.processed, k=2) + } else stop("unknown method") } diff --git a/lib/transform.rb b/lib/transform.rb index 8fe1093..f6f769d 100644 --- a/lib/transform.rb +++ b/lib/transform.rb @@ -396,8 +396,8 @@ module OpenTox @q_prop = gsl_q_prop_orig.row(0).to_a end - LOGGER.debug "F: #{@n_prop.size}x#{@n_prop[0].size}; R: #{@q_prop.size}" - LOGGER.debug "Sims: #{@sims.size}, Acts: #{@acts.size}" + LOGGER.debug "F: #{@n_prop.size}x#{@n_prop[0].size}; R: #{@q_prop.size}" if (@n_prop && @n_prop[0] && @q_prop) + LOGGER.debug "Sims: #{@sims.size}, Acts: #{@acts.size}" if (@sims && @acts) @sims = [ gram_matrix, @sims ] diff --git a/opentox-ruby.gemspec b/opentox-ruby.gemspec index ca2d397..d3ae2d7 100644 --- a/opentox-ruby.gemspec +++ b/opentox-ruby.gemspec @@ -5,24 +5,25 @@ Gem::Specification.new do |s| s.name = %q{opentox-ruby} - s.version = "3.1.0" + s.version = "2.0.1" s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version= s.authors = ["Christoph Helma, Martin Guetlein, Andreas Maunz, Micha Rautenberg, David Vorgrimmler"] - s.date = %q{2012-03-26} + s.date = %q{2011-06-15} s.description = %q{Ruby wrapper for the OpenTox REST API (http://www.opentox.org)} s.email = %q{helma@in-silico.ch} + s.executables = ["opentox-install-debian.sh", "opentox-install-ubuntu.sh"] s.extra_rdoc_files = [ - "ChangeLog", "LICENSE", "README.markdown" ] s.files = [ - "ChangeLog", "LICENSE", "README.markdown", "Rakefile", "VERSION", + "bin/opentox-install-debian.sh", + "bin/opentox-install-ubuntu.sh", "lib/algorithm.rb", "lib/authorization.rb", "lib/compound.rb", @@ -40,126 +41,121 @@ Gem::Specification.new do |s| "lib/overwrite.rb", "lib/parser.rb", "lib/policy.rb", - "lib/r-util.rb", "lib/rest_client_wrapper.rb", "lib/serializer.rb", "lib/spork.rb", - "lib/stratification.R", "lib/task.rb", "lib/templates/default_guest_policy.xml", "lib/templates/default_policy.xml", "lib/to-html.rb", "lib/transform.rb", - "lib/utils.rb", + "lib/utils.rb" "lib/validation.rb" ] - s.homepage = %q{http://github.com/opentox/opentox-ruby} + s.homepage = %q{http://github.com/helma/opentox-ruby} s.require_paths = ["lib"] - s.rubygems_version = %q{1.5.3} + s.rubygems_version = %q{1.5.2} s.summary = %q{Ruby wrapper for the OpenTox REST API} if s.respond_to? :specification_version then s.specification_version = 3 if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then - s.add_runtime_dependency(%q<sinatra>, ["= 1.2.6"]) - s.add_runtime_dependency(%q<emk-sinatra-url-for>, ["= 0.2.1"]) - s.add_runtime_dependency(%q<sinatra-respond_to>, ["= 0.7.0"]) - s.add_runtime_dependency(%q<sinatra-static-assets>, ["= 0.5.0"]) - s.add_runtime_dependency(%q<rest-client>, ["= 1.6.1"]) - s.add_runtime_dependency(%q<rack>, ["= 1.3.5"]) - s.add_runtime_dependency(%q<rack-contrib>, ["= 1.1.0"]) - s.add_runtime_dependency(%q<rack-flash>, ["= 0.1.1"]) - s.add_runtime_dependency(%q<nokogiri>, ["= 1.4.4"]) - s.add_runtime_dependency(%q<rubyzip>, ["= 0.9.4"]) - s.add_runtime_dependency(%q<roo>, ["= 1.9.3"]) - s.add_runtime_dependency(%q<spreadsheet>, ["= 0.6.5.4"]) - s.add_runtime_dependency(%q<google-spreadsheet-ruby>, ["= 0.1.5"]) - s.add_runtime_dependency(%q<yajl-ruby>, ["= 0.8.2"]) - s.add_runtime_dependency(%q<rinruby>, ["= 2.0.2"]) - s.add_runtime_dependency(%q<ohm>, ["= 0.1.3"]) - s.add_runtime_dependency(%q<ohm-contrib>, ["= 0.1.1"]) - s.add_runtime_dependency(%q<SystemTimer>, ["= 1.2.3"]) - s.add_runtime_dependency(%q<rjb>, ["= 1.3.4"]) - s.add_runtime_dependency(%q<haml>, ["= 3.1.1"]) - s.add_runtime_dependency(%q<akephalos>, ["= 0.2.5"]) - s.add_runtime_dependency(%q<dm-core>, ["= 1.1.0"]) - s.add_runtime_dependency(%q<dm-serializer>, ["= 1.1.0"]) - s.add_runtime_dependency(%q<dm-timestamps>, ["= 1.1.0"]) - s.add_runtime_dependency(%q<dm-types>, ["= 1.1.0"]) - s.add_runtime_dependency(%q<dm-migrations>, ["= 1.1.0"]) - s.add_runtime_dependency(%q<dm-validations>, ["= 1.1.0"]) - s.add_runtime_dependency(%q<dm-sqlite-adapter>, ["= 1.1.0"]) - s.add_runtime_dependency(%q<ruby-plot>, ["= 0.6.0"]) - s.add_runtime_dependency(%q<gsl>, ["= 1.14.7"]) - s.add_runtime_dependency(%q<statsample>, ["= 1.1.0"]) + s.add_runtime_dependency(%q<sinatra>, [">= 0"]) + s.add_runtime_dependency(%q<emk-sinatra-url-for>, [">= 0"]) + s.add_runtime_dependency(%q<sinatra-respond_to>, [">= 0"]) + s.add_runtime_dependency(%q<sinatra-static-assets>, [">= 0"]) + s.add_runtime_dependency(%q<rest-client>, [">= 0"]) + s.add_runtime_dependency(%q<rack>, [">= 0"]) + s.add_runtime_dependency(%q<rack-contrib>, [">= 0"]) + s.add_runtime_dependency(%q<rack-flash>, [">= 0"]) + s.add_runtime_dependency(%q<nokogiri>, [">= 0"]) + s.add_runtime_dependency(%q<rubyzip>, [">= 0"]) + s.add_runtime_dependency(%q<roo>, [">= 0"]) + s.add_runtime_dependency(%q<spreadsheet>, [">= 0"]) + s.add_runtime_dependency(%q<google-spreadsheet-ruby>, [">= 0"]) + s.add_runtime_dependency(%q<yajl-ruby>, [">= 0"]) + s.add_runtime_dependency(%q<tmail>, [">= 0"]) + s.add_runtime_dependency(%q<rinruby>, [">= 0"]) + s.add_runtime_dependency(%q<ohm>, [">= 0"]) + s.add_runtime_dependency(%q<ohm-contrib>, [">= 0"]) + s.add_runtime_dependency(%q<SystemTimer>, [">= 0"]) + s.add_runtime_dependency(%q<rjb>, [">= 0"]) + s.add_runtime_dependency(%q<dm-core>, [">= 0"]) + s.add_runtime_dependency(%q<dm-serializer>, [">= 0"]) + s.add_runtime_dependency(%q<dm-timestamps>, [">= 0"]) + s.add_runtime_dependency(%q<dm-types>, [">= 0"]) + s.add_runtime_dependency(%q<dm-migrations>, [">= 0"]) + s.add_runtime_dependency(%q<dm-validations>, [">= 0"]) + s.add_runtime_dependency(%q<dm-sqlite-adapter>, [">= 0"]) + s.add_runtime_dependency(%q<haml>, [">= 3"]) + s.add_runtime_dependency(%q<ruby-plot>, ["~> 0.4.0"]) + s.add_runtime_dependency(%q<statsample>, [">= 0"]) s.add_development_dependency(%q<jeweler>, [">= 0"]) else - s.add_dependency(%q<sinatra>, ["= 1.2.6"]) - s.add_dependency(%q<emk-sinatra-url-for>, ["= 0.2.1"]) - s.add_dependency(%q<sinatra-respond_to>, ["= 0.7.0"]) - s.add_dependency(%q<sinatra-static-assets>, ["= 0.5.0"]) - s.add_dependency(%q<rest-client>, ["= 1.6.1"]) - s.add_dependency(%q<rack>, ["= 1.3.5"]) - s.add_dependency(%q<rack-contrib>, ["= 1.1.0"]) - s.add_dependency(%q<rack-flash>, ["= 0.1.1"]) - s.add_dependency(%q<nokogiri>, ["= 1.4.4"]) - s.add_dependency(%q<rubyzip>, ["= 0.9.4"]) - s.add_dependency(%q<roo>, ["= 1.9.3"]) - s.add_dependency(%q<spreadsheet>, ["= 0.6.5.4"]) - s.add_dependency(%q<google-spreadsheet-ruby>, ["= 0.1.5"]) - s.add_dependency(%q<yajl-ruby>, ["= 0.8.2"]) - s.add_dependency(%q<rinruby>, ["= 2.0.2"]) - s.add_dependency(%q<ohm>, ["= 0.1.3"]) - s.add_dependency(%q<ohm-contrib>, ["= 0.1.1"]) - s.add_dependency(%q<SystemTimer>, ["= 1.2.3"]) - s.add_dependency(%q<rjb>, ["= 1.3.4"]) - s.add_dependency(%q<haml>, ["= 3.1.1"]) - s.add_dependency(%q<akephalos>, ["= 0.2.5"]) - s.add_dependency(%q<dm-core>, ["= 1.1.0"]) - s.add_dependency(%q<dm-serializer>, ["= 1.1.0"]) - s.add_dependency(%q<dm-timestamps>, ["= 1.1.0"]) - s.add_dependency(%q<dm-types>, ["= 1.1.0"]) - s.add_dependency(%q<dm-migrations>, ["= 1.1.0"]) - s.add_dependency(%q<dm-validations>, ["= 1.1.0"]) - s.add_dependency(%q<dm-sqlite-adapter>, ["= 1.1.0"]) - s.add_dependency(%q<ruby-plot>, ["= 0.6.0"]) - s.add_dependency(%q<gsl>, ["= 1.14.7"]) - s.add_dependency(%q<statsample>, ["= 1.1.0"]) + s.add_dependency(%q<sinatra>, [">= 0"]) + s.add_dependency(%q<emk-sinatra-url-for>, [">= 0"]) + s.add_dependency(%q<sinatra-respond_to>, [">= 0"]) + s.add_dependency(%q<sinatra-static-assets>, [">= 0"]) + s.add_dependency(%q<rest-client>, [">= 0"]) + s.add_dependency(%q<rack>, [">= 0"]) + s.add_dependency(%q<rack-contrib>, [">= 0"]) + s.add_dependency(%q<rack-flash>, [">= 0"]) + s.add_dependency(%q<nokogiri>, [">= 0"]) + s.add_dependency(%q<rubyzip>, [">= 0"]) + s.add_dependency(%q<roo>, [">= 0"]) + s.add_dependency(%q<spreadsheet>, [">= 0"]) + s.add_dependency(%q<google-spreadsheet-ruby>, [">= 0"]) + s.add_dependency(%q<yajl-ruby>, [">= 0"]) + s.add_dependency(%q<tmail>, [">= 0"]) + s.add_dependency(%q<rinruby>, [">= 0"]) + s.add_dependency(%q<ohm>, [">= 0"]) + s.add_dependency(%q<ohm-contrib>, [">= 0"]) + s.add_dependency(%q<SystemTimer>, [">= 0"]) + s.add_dependency(%q<rjb>, [">= 0"]) + s.add_dependency(%q<dm-core>, [">= 0"]) + s.add_dependency(%q<dm-serializer>, [">= 0"]) + s.add_dependency(%q<dm-timestamps>, [">= 0"]) + s.add_dependency(%q<dm-types>, [">= 0"]) + s.add_dependency(%q<dm-migrations>, [">= 0"]) + s.add_dependency(%q<dm-validations>, [">= 0"]) + s.add_dependency(%q<dm-sqlite-adapter>, [">= 0"]) + s.add_dependency(%q<haml>, [">= 3"]) + s.add_dependency(%q<ruby-plot>, ["~> 0.4.0"]) + s.add_dependency(%q<statsample>, [">= 0"]) s.add_dependency(%q<jeweler>, [">= 0"]) end else - s.add_dependency(%q<sinatra>, ["= 1.2.6"]) - s.add_dependency(%q<emk-sinatra-url-for>, ["= 0.2.1"]) - s.add_dependency(%q<sinatra-respond_to>, ["= 0.7.0"]) - s.add_dependency(%q<sinatra-static-assets>, ["= 0.5.0"]) - s.add_dependency(%q<rest-client>, ["= 1.6.1"]) - s.add_dependency(%q<rack>, ["= 1.3.5"]) - s.add_dependency(%q<rack-contrib>, ["= 1.1.0"]) - s.add_dependency(%q<rack-flash>, ["= 0.1.1"]) - s.add_dependency(%q<nokogiri>, ["= 1.4.4"]) - s.add_dependency(%q<rubyzip>, ["= 0.9.4"]) - s.add_dependency(%q<roo>, ["= 1.9.3"]) - s.add_dependency(%q<spreadsheet>, ["= 0.6.5.4"]) - s.add_dependency(%q<google-spreadsheet-ruby>, ["= 0.1.5"]) - s.add_dependency(%q<yajl-ruby>, ["= 0.8.2"]) - s.add_dependency(%q<rinruby>, ["= 2.0.2"]) - s.add_dependency(%q<ohm>, ["= 0.1.3"]) - s.add_dependency(%q<ohm-contrib>, ["= 0.1.1"]) - s.add_dependency(%q<SystemTimer>, ["= 1.2.3"]) - s.add_dependency(%q<rjb>, ["= 1.3.4"]) - s.add_dependency(%q<haml>, ["= 3.1.1"]) - s.add_dependency(%q<akephalos>, ["= 0.2.5"]) - s.add_dependency(%q<dm-core>, ["= 1.1.0"]) - s.add_dependency(%q<dm-serializer>, ["= 1.1.0"]) - s.add_dependency(%q<dm-timestamps>, ["= 1.1.0"]) - s.add_dependency(%q<dm-types>, ["= 1.1.0"]) - s.add_dependency(%q<dm-migrations>, ["= 1.1.0"]) - s.add_dependency(%q<dm-validations>, ["= 1.1.0"]) - s.add_dependency(%q<dm-sqlite-adapter>, ["= 1.1.0"]) - s.add_dependency(%q<ruby-plot>, ["= 0.6.0"]) - s.add_dependency(%q<gsl>, ["= 1.14.7"]) - s.add_dependency(%q<statsample>, ["= 1.1.0"]) + s.add_dependency(%q<sinatra>, [">= 0"]) + s.add_dependency(%q<emk-sinatra-url-for>, [">= 0"]) + s.add_dependency(%q<sinatra-respond_to>, [">= 0"]) + s.add_dependency(%q<sinatra-static-assets>, [">= 0"]) + s.add_dependency(%q<rest-client>, [">= 0"]) + s.add_dependency(%q<rack>, [">= 0"]) + s.add_dependency(%q<rack-contrib>, [">= 0"]) + s.add_dependency(%q<rack-flash>, [">= 0"]) + s.add_dependency(%q<nokogiri>, [">= 0"]) + s.add_dependency(%q<rubyzip>, [">= 0"]) + s.add_dependency(%q<roo>, [">= 0"]) + s.add_dependency(%q<spreadsheet>, [">= 0"]) + s.add_dependency(%q<google-spreadsheet-ruby>, [">= 0"]) + s.add_dependency(%q<yajl-ruby>, [">= 0"]) + s.add_dependency(%q<tmail>, [">= 0"]) + s.add_dependency(%q<rinruby>, [">= 0"]) + s.add_dependency(%q<ohm>, [">= 0"]) + s.add_dependency(%q<ohm-contrib>, [">= 0"]) + s.add_dependency(%q<SystemTimer>, [">= 0"]) + s.add_dependency(%q<rjb>, [">= 0"]) + s.add_dependency(%q<dm-core>, [">= 0"]) + s.add_dependency(%q<dm-serializer>, [">= 0"]) + s.add_dependency(%q<dm-timestamps>, [">= 0"]) + s.add_dependency(%q<dm-types>, [">= 0"]) + s.add_dependency(%q<dm-migrations>, [">= 0"]) + s.add_dependency(%q<dm-validations>, [">= 0"]) + s.add_dependency(%q<dm-sqlite-adapter>, [">= 0"]) + s.add_dependency(%q<haml>, [">= 3"]) + s.add_dependency(%q<ruby-plot>, ["~> 0.4.0"]) + s.add_dependency(%q<statsample>, [">= 0"]) s.add_dependency(%q<jeweler>, [">= 0"]) end end |