ngs_server 0.6 → 0.7

data/README.md

@@ -41,6 +41,19 @@ invoke file: genotypes.vcf.gz with coordinates 1073361 to 1238825 on chromosome
 
 * http://0.0.0.0:4569/json/vcf/genotypes.vcf.gz?segment=1&min=1073361&max=1238825
 
+## find data
+
+find data sources that have been added
+
+    # ngs_server find <dir> <regex>
+    ngs_server find . *  # return everything
+    
+    # return found data as link to view in Rover
+    ngs_server find . "*bam" -r 1:1:100000
+    
+    # specify server url that ngs_server is running on
+    # so the correct links to sources will be generated
+    ngs_server find . "*bam" -r 1:1:100000 -s http://mydataserver.com
 
 ## Example
     # create data directory
@@ -55,9 +68,23 @@ invoke file: genotypes.vcf.gz with coordinates 1073361 to 1238825 on chromosome
     ngs_server add example-data/
     
     # start server
-    ngs_server start -p 4569
+    ngs_server start -d
     
+    # find data
+    ngs_server find . "*bam"
+    
+    # generate Rover url to view data
+    # -r chr:min:max
+    ngs_server find . "*bam" -r 22:14596532:14699000
+    # and then just paste the generate url into a browser
+    
+    # to make things quicker you can open the link from
+    # the command line in Google Chrome (Mac only, but linux is similar)
+    open -a "Google Chrome" $(ngs_server find . "*bam" -r 22:14596532:14699000)
+    
+    # to see the pure json that ngs_server sends
     # paste following url in browser
-    # to download region of bam as json in web browser
     # http://0.0.0.0:4569/json/bam/example-data/small.bam?min=14596532&max=14699000&segment=22
-    
+    
+    # stop server
+    ngs_server stop

data/bin/ngs_server

@@ -14,6 +14,10 @@
 
   options = {}
   command = ""
+  extensions = {
+    ".bam" => "bam",
+    ".gz"  => "vcf"
+  }
 
   optparse = OptionParser.new do |opts|
     opts.banner = "Usage: ngs_server start|stop|add [options]"
@@ -41,6 +45,15 @@
         options[:daemonize] = "-d";
     end
     
+    opts.on( '-r', '--rover REGION:MIN:MAX', 'returns link to Rover to display all matches' ) do |f|
+        options[:rover] = f;
+    end
+    
+    options[:serverurl] = "http://0.0.0.0:" + options[:port]
+    opts.on( '-s', '--serverurl URL', 'the url for the server to access the data' ) do |f|
+        options[:serverurl] = f;
+    end
+    
     # opts.on( '-C', '--config', 'configuration file for Thin server' ) do |f|
     #     options[:config] = f;
     # end
@@ -49,8 +62,7 @@
   
   optparse.parse!
   command = ARGV[0]
-  
-  
+
 
   if (command == 'start')
    # ngsrun options
@@ -66,15 +78,65 @@
    #NgsServer.run!
   elsif (command == 'stop')
     rackup_path = File.join(path, '../lib/config.ru')
+    puts "Stopping Ngs_Server ..."
     `thin -R #{rackup_path} -p #{options[:port]} stop`
   elsif (command == 'add')
-    # source_path = File.absolute_path(ARGV[1])
-    # puts source_path
-    # file_name = File.basename(source_path)
-    # puts file_name
-    # data_dir_path = File.join(path,'../data', file_name)
-    # puts data_dir_path
-    # `ln -s #{source_path} #{data_dir_path}`
     ngsadd ARGV[1]
+  elsif (command == 'find')
+
+    data_path = File.join(path, '../data')
+    
+    if ARGV[1]
+      dir = ARGV[1]
+    else
+      dir = "."
+    end
+    
+    if ARGV[2]
+      expr = ARGV[2]
+    else
+      expr = "*"
+    end
+
+    Dir.chdir(data_path)
+    sources = `find -L #{dir} -iname "#{expr}"`.split("\n")
+    
+    curated_sources = Array.new
+    sources.each do |source|
+      if (File.extname(source) == ".bam" || File.extname(File.basename(source, ".gz")) == ".vcf")
+        curated_sources.push source
+      end
+    end
+    
+
+    if (!options[:rover].nil?)
+      rover_url = "http://chmille4.github.com/Rover/index.html"
+      
+      names_url = "names=" + curated_sources.join(',')
+      
+      data_urls = []
+      curated_sources.each do |s|
+        str = options[:serverurl] + "/json/"
+        str += extensions[ File.extname(s) ] + "/"
+        str += s        
+        data_urls.push(str)
+      end
+      data_url =  "urls=" + data_urls.join(',')
+      
+      segment, min, max = options[:rover].split(":")
+      segment_url = "segment=" + segment
+      min_url = "min=" + min
+      max_url = "max=" + max
+      
+      display_url = "display=" + Array.new(curated_sources.size) { |i| "collapse" }.join(',')
+      types_url = "types=" + Array.new(curated_sources.size) { |i| "" }.join(',')
+      
+      params_url = [names_url, data_url, segment_url, min_url, max_url, display_url, types_url].join('&')
+      
+      puts rover_url + "?" + params_url
+    else
+      puts curated_sources
+    end
+    
   end
   

data/lib/ngs_server/version.rb

@@ -1,3 +1,3 @@
 module NgsServer
-  VERSION = "0.6"
+  VERSION = "0.7"
 end

data/lib/ngs_server.rb

@@ -40,14 +40,19 @@ class MyNgsServer < Sinatra::Base
 
   end
 
-  get '/json/sources/:extension' do
+  get '/json/sources/*' do |path|
 
     # turn off json content type so a preflight cors doesn't need to be done
     # content_type :json
     response['Access-Control-Allow-Origin'] = '*';
 
+    extension = File.basename(path)
+    dirpath = File.dirname(path)    
+    
+    private_dir = "private"
+
     # invoke with eg: base_url/json/vcf/file=ALL.2of4intersection.20100804.sites.vcf.gz?min=6992179&max=6992190&segment=1
-    list  = `find -L #{datapath} -name '*#{params['extension']}' | awk -F#{datapath}/ '{print $2}'`
+    list  = `find -L #{datapath}/#{dirpath} -not \\( -name private -prune \\) -name '*#{extension}' | awk -F#{datapath}/ '{print $2}'`
     list.split("\n").to_json
 
   end

metadata

@@ -2,7 +2,7 @@
 name: ngs_server
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: "0.6"
+  version: "0.7"
 platform: ruby
 authors: 
 - Chase Miller
@@ -10,7 +10,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2012-01-12 00:00:00 -05:00
+date: 2012-01-31 00:00:00 -05:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency