bio-basespace-sdk 0.1.2 → 0.1.3

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 92cef1459a52d87689eb5ce456fc464292de4019
+  data.tar.gz: a123635b332ca349729b113e307e171819c725a6
+SHA512:
+  metadata.gz: 32b9ea9d704f55d3c6496d33cd353b5eff3e7ad213cd4658eeee6e212aa40231bedd445e41b2b55a2048f1e53581ecf0a53f302e27491a3da036ac6e2105af9d
+  data.tar.gz: 9affe81766270bb7631cde418188d31cb62b7f6ef4046fda52f2aab72cfc9d8e165a93e87ed4b8dba9398451fcbcb6ae4a00c7dd8a5a557840dfafb1fb79aeb9

data/Gemfile

@@ -8,7 +8,7 @@ gem "addressable", ">= 2.3.2"
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
 group :development do
-  gem "rspec", "~> 2.8.0"
+  gem "rspec", "~> 2.14.1"
   gem "bundler", ">= 1.1.5"
   gem "jeweler", "~> 1.8.4"
   gem "bio", ">= 1.4.2"

data/README.md

@@ -8,7 +8,19 @@ The primary purpose of the SDK is to provide an easy-to-use Ruby environment ena
 
 ## Availability
 
-Current version of ``Bio::BaseSpace`` can be checked out here:
+*Note:* We are still testing our code. Please take the production-ready gem with a pinch of salt.
+
+The production environment version of ``Bio::BaseSpace`` is available as a Ruby gem:
+
+  gem install bio-basespace-sdk
+
+Depending on your Ruby installation, it might be necessary to install the Ruby gem with superuser permissions:
+
+  sudo gem install bio-basespace-sdk
+
+### Pre-Release Version
+
+The pre-release version of ``Bio::BaseSpace`` can be checked out here:
 
 	git clone https://github.com/joejimbo/basespace-ruby-sdk.git
 
@@ -16,7 +28,7 @@ or by,
 
 	git clone git@github.com:joejimbo/basespace-ruby-sdk.git
 
-*Note:* We will make the SDK available as a Ruby gem when our implementation is production ready. It will then also be listed on [Biogems.info](http://www.biogems.info).
+Status: [![Build Status](https://travis-ci.org/joejimbo/basespace-ruby-sdk.png?branch=master)](https://travis-ci.org/joejimbo/basespace-ruby-sdk)
 
 ## Setup
 
@@ -33,7 +45,7 @@ or add it to your Ruby scripts using Bio::BaseSpace:
 To test that everything is working as expected, launch a Interactive Ruby and try importing 'Bio::BaseSpace': 
 
 	$ irb
-	>> require 'basespace'
+	>> require 'bio-basespace-sdk'
 	>> include Bio::BaseSpace
 
 ## Application triggering
@@ -46,7 +58,7 @@ we are able to obtain information about the user who launched the App and the da
 First, we instantiate a BaseSpaceAPI object using the ``client_key`` and ``client_secret`` codes provided on the BaseSpace developer's website when registering our App, as well as the ``AppSessionId`` generated from the app-triggering: 
 
 
-	require 'basespace'
+	require 'bio-basespace-sdk'
 	
 	include Bio::BaseSpace
 	
@@ -184,7 +196,7 @@ Here we demonstrate the basic BaseSpace authentication process. The work-flow ou
 
 Again, we will start out by initializing a ``BaseSpaceAPI`` object:
 
-	require 'basespace'
+	require 'bio-basespace-sdk'
 	include Bio::BaseSpace
 
 	client_id       = 'my client key'
@@ -266,7 +278,7 @@ a ``user`` instance we can use it to retrieve all project belonging to that user
 
 First we will initialize a ``BaseSpaceAPI`` using our access-token for ``global browse``:
 
-	require 'basespace'
+	require 'bio-basespace-sdk'
 	include Bio::BaseSpace
 
 	# REST server information and user access_token 
@@ -372,7 +384,7 @@ In addition, we take a look at some of the special queuring methods associated w
 Again, start out by initializing a ``BaseSpaceAPI`` instance and retrieving all projects belonging to the current user:
 
 	# First, create a client for making calls for this user session 
-	require 'basespace'
+	require 'bio-basespace-sdk'
 	include Bio::BaseSpace
 
 	client_id       = 'my client key'

data/VERSION

@@ -1 +1 @@
-0.1.2
+0.1.3

data/examples/0_app_triggering.rb

@@ -16,7 +16,7 @@
 # Application triggering
 #   https://developer.basespace.illumina.com/docs/content/documentation/sdk-samples/python-sdk-overview#Application_triggering
 
-require 'basespace'
+require 'bio-basespace-sdk'
 
 include Bio::BaseSpace
 

data/examples/1_authentication.rb

@@ -16,7 +16,7 @@
 # Requesting an access-token for data browsing
 #   https://developer.basespace.illumina.com/docs/content/documentation/sdk-samples/python-sdk-overview#Requesting_an_access-token_for_data_browsing
 
-require 'basespace'
+require 'bio-basespace-sdk'
 
 include Bio::BaseSpace
 

data/examples/2_browsing.rb

@@ -16,7 +16,7 @@
 # Browsing data with global browse access
 #   https://developer.basespace.illumina.com/docs/content/documentation/sdk-samples/python-sdk-overview#Browsing_data_with_global_browse_access
 
-require 'basespace'
+require 'bio-basespace-sdk'
 
 include Bio::BaseSpace
 

data/examples/3_accessing_files.rb

@@ -16,7 +16,7 @@
 # Accessing file-trees and querying BAM or VCF files
 #   https://developer.basespace.illumina.com/docs/content/documentation/sdk-samples/python-sdk-overview#Accessing_file-trees_and_querying_BAM_or_VCF_files
 
-require 'basespace'
+require 'bio-basespace-sdk'
 
 include Bio::BaseSpace
 

data/examples/4_app_result_upload.rb

@@ -16,7 +16,7 @@
 # Creating an AppResult and uploading files
 #   https://developer.basespace.illumina.com/docs/content/documentation/sdk-samples/python-sdk-overview#Creating_an_AppResult_and_uploading_files
 
-require 'basespace'
+require 'bio-basespace-sdk'
 
 include Bio::BaseSpace
 

data/examples/5_purchasing.rb

@@ -13,7 +13,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-require 'basespace'
+require 'bio-basespace-sdk'
 
 include Bio::BaseSpace
 

data/lib/basespace/model/multipart_upload.rb

@@ -31,7 +31,7 @@ class UploadTask
   # +total+:: Total number of parts in the multi-part upload.
   # +myfile+:: Local file to be uploaded.
   # +attempt+:: Number of attempts that the file was previously uploaded (upload tries).
-  def initialize(self, api, bs_file_id, part, total, myfile, attempt)
+  def initialize(api, bs_file_id, part, total, myfile, attempt)
     @api         = api
     @part        = part       # part number
     @total       = total       # out of total part count
@@ -75,12 +75,17 @@ class UploadTask
   end
 
 end # class UploadTask
-    
-class Consumer  # [TODO] inherit multiprocessing.Process
+
+# Multipart file upload consumer class.
+#
+# TODO This file is not yet ported as the multipartFileUpload class is
+# just mentioned in the comment section of the BaseSpaceAPI file.
+class Consumer
+
   def initialize(task_queue, result_queue, pause_event, halt_event)
-    # [TODO] http://stackoverflow.com/questions/710785/working-with-multiple-processes-in-ruby
-    #        http://stackoverflow.com/questions/855805/please-introduce-a-multi-processing-library-in-perl-or-ruby
-    #        http://docs.python.jp/2.6/library/multiprocessing.html
+    # TODO http://stackoverflow.com/questions/710785/working-with-multiple-processes-in-ruby
+    #      http://stackoverflow.com/questions/855805/please-introduce-a-multi-processing-library-in-perl-or-ruby
+    #      http://docs.python.jp/2.6/library/multiprocessing.html
     #multiprocessing.Process.__init__(self)
     @task_queue    = task_queue
     @result_queue  = result_queue
@@ -88,43 +93,46 @@ class Consumer  # [TODO] inherit multiprocessing.Process
     @halt          = haltEvent
   end
   
-  # [TODO]
+  # TODO
   def run
     proc_name = self.name
-    while True:
+    while True
       unless self.pause.is_set()
         next_task = self.task_queue.get()
       end
             
-      if next_task is None or self.halt.is_set(): # check if we are out of jobs or have been halted
+      if next_task is None or self.halt.is_set() # check if we are out of jobs or have been halted
         # Poison pill means shutdown
-        print '%s: Exiting' % proc_name
+        puts "#{proc_name}: Exiting"
         self.task_queue.task_done()
         break
-      elsif self.pause.is_set():                   # if we have been paused, sleep for a bit then check back
-        print '%s: Paused' % proc_name 
+      elsif self.pause.is_set()                   # if we have been paused, sleep for a bit then check back
+        puts "#{proc_name}: Paused"
         time.sleep(3)                                       
-      else:                                       # do some work
-        print '%s: %s' % (proc_name, next_task)
+      else                                       # do some work
+        puts "#{proc_name}: #{next_task}"
         answer = next_task()
         self.task_queue.task_done()
-        if answer.state == 1:                   # case everything went well
+        if answer.state == 1                   # case everything went well
           self.result_queue.put(answer)
-        else:                                   # case something sent wrong
-          if next_task.attempt < 3:
+        else                                   # case something sent wrong
+          if next_task.attempt < 3
             self.task_queue.put(next_task)  # queue the guy for a retry
-          else:                               # problems, shutting down this party
+          else                               # problems, shutting down this party
             self.halt.set()                 # halt all other process
           end
         end
       end
     end
-    return
   end
 end # class Consumer
 
+# Multipart file upload class.
+#
+# TODO This file is not yet ported as the multipartFileUpload class is
+# just mentioned in the comment section of the BaseSpaceAPI file.
+class MultipartUpload
 
-class MultipartUpload:
   def initialize(api, a_id, local_file, file_object, cpu_count, part_size, temp_dir, verbose)
     @api            = api
     @analysis_id    = a_id
@@ -141,13 +149,14 @@ class MultipartUpload:
   end
 
   def to_s
-    # [TODO] fix this.
+    # TODO fix this.
+    # NOTE Python sublist notation [:5] already changed to Ruby [0..4]
     return "MPU -  Stat: " + @status +  ", LiveThread: " + str(self.getRunningThreadCount()) + \
-                ", RunTime: " + str(self.getRunningTime())[:5] + 's' + \
+                ", RunTime: " + str(self.getRunningTime())[0..4] + 's' + \
                 ", Q-size " + str(self.tasks.qsize()) + \
                 ", Completed " + str(self.getProgressRatio()) + \
                 ", AVG TransferRate " + self.getTransRate() + \
-                ", Data transfered " + str(self.getTotalTransfered())[:5] + 'Gb'
+                ", Data transfered " + str(self.getTotalTransfered())[0..4] + 'Gb'
   end
     
   def to_str
@@ -165,7 +174,7 @@ class MultipartUpload:
     totalSize = os.path.getsize(self.localFile)
     fileCount = int(math.ceil(totalSize/(self.partSize*1024.0*1000)))
     
-    if self.verbose: 
+    if self.verbose 
       print "TotalSize " + str(totalSize)
       print "Using split size " + str(self.partSize) +"Mb"
       print "Filecount " + str(fileCount)
@@ -175,110 +184,118 @@ class MultipartUpload:
     # Establish communication queues
     self.tasks = multiprocessing.JoinableQueue()
     self.completedPool = multiprocessing.Queue()
-    for i in xrange(1,fileCount+1):         # set up the task queue
-      t = uploadTask(self.api,self.remoteFile.Id,i, fileCount, self.localFile, 0)
+    [1..fileCount].each { |i|         # set up the task queue
+      t = uploadTask(self.api,self.remoteFile.Id, i, fileCount, self.localFile, 0)
       self.tasks.put(t)
-    end
+    }
     self.totalTask  = self.tasks.qsize()
     
     # create consumers
     self.pauseEvent = multiprocessing.Event()
     self.haltEvent = multiprocessing.Event()
-    if self.verbose:
+    if self.verbose
       print 'Creating %d consumers' % self.cpuCount
       print "queue size " + str(self.tasks.qsize())
     end
-    self.consumers = [ Consumer(self.tasks, self.completedPool,self.pauseEvent,self.haltEvent) for i in xrange(self.cpuCount) ]
-      for c in self.consumers: self.tasks.put(None)   # add poisson pill
-    end
+    # NOTE Original code -- note the strange indent. Variables i and c not used. Buggy code?
+    # self.consumers = [ Consumer(self.tasks, self.completedPool,self.pauseEvent,self.haltEvent) for i in xrange(self.cpuCount) ]
+    #   for c in self.consumers: self.tasks.put(None)   # add poisson pill
+    self.consumers = [0..self.cpuCount].map { |i| Consumer(self.tasks, self.completedPool, self.pauseEvent, self.haltEvent) }
+    self.consumers.each { |c| self.tasks.put(nil) }
   end
         
-  def __cleanUp__(self):
+  def __cleanUp__
     self.stats[0] += 1
   end
     
-  def startUpload(self,returnOnFinish=0,testInterval=5):
-    if self.Status=='Terminated' or self.Status=='Completed':
-      raise Exception('Cannot resume a ' + self.Status + ' multi-part upload session.')
+  def startUpload(returnOnFinish = 0, testInterval = 5)
+    raise Exception('Cannot resume a ' + self.Status + ' multi-part upload session.') if self.Status == 'Terminated' or self.Status == 'Completed'
         
-    if self.Status == 'Initialized':
+    if self.Status == 'Initialized'
       self.StartTime = time.time()
-      for w in self.consumers:
+      self.consumers.each { |w|
         w.start()
-    if self.Status == 'Paused':
+      }
+    elsif self.Status == 'Paused'
       self.pauseEvent.clear()
+    end
     self.Status = 'Running'
         
     # If returnOnFinish is set 
-    if returnOnFinish:
+    if returnOnFinish
       i=0
-      while not self.hasFinished():
-        if self.verbose and i: print str(i) + ': ' + str(self)
+      while not self.hasFinished()
+        print str(i) + ': ' + str(self) if self.verbose and i
         time.sleep(testInterval)
         i+=1
+      end
       self.finalize()
       return 1
-    else:
+    else
       return 1
     end
   end
     
-  def finalize(self):
-    if self.getRunningThreadCount():
-      raise Exception('Cannot finalize a transfer with running threads.')
-    if self.Status=='Running':
+  def finalize
+    raise Exception('Cannot finalize a transfer with running threads.') if self.getRunningThreadCount()
+    if self.Status=='Running'
       # code here for 
       self.Status=='Completed'
-    else:
+    else
       raise Exception('To finalize the status of the transfer must be "Running."')
     end
   end
     
-  def hasFinished(self):
-    if self.Status == 'Initialized': return 0
-    return not self.getRunningThreadCount()>0
+  def hasFinished
+    return 0 if self.Status == 'Initialized'
+    return !(self.getRunningThreadCount() > 0)
   end
     
-  def pauseUpload(self):
+  def pauseUpload
     self.pauseEvent.set()
     self.Status = 'Paused'
   end
     
-  def haltUpload(self):
-    for c in self.consumers: c.terminate()
+  def haltUpload
+    self.consumers.each { |c| c.terminate() }
     self.Status = 'Terminated'
   end
     
-  def getStatus(self):
+  def getStatus
     return self.Status
   end
     
-  def getFileResponse(self):
+  def getFileResponse
     return self.remoteFile
   end
     
-  def getRunningThreadCount(self):
-    return sum([c.is_alive() for c in self.consumers])
+  def getRunningThreadCount
+    return sum(self.consumers.map { |c| c.is_alive() })
   end
 
-  def getTransRate(self):
+  def getTransRate
     # tasks completed                        size of file-parts 
-    return str((self.totalTask - self.tasks.qsize())*self.partSize/self.getRunningTime())[:6] + ' mb/s'
+    # NOTE Python sublist [:6] already ported to Ruby [0..5]
+    return str((self.totalTask - self.tasks.qsize())*self.partSize/self.getRunningTime())[0..5] + ' mb/s'
   end
     
-  def getRunningTime(self):
-    if self.StartTime==-1: return 0
-    else: return time.time() - self.StartTime
+  def getRunningTime
+    if self.StartTime==-1
+      return 0
+    else
+      return time.time() - self.StartTime
+    end
   end
   
   # Returns the total data amoun transfered in Gb
-  def getTotalTransfered(self):
-    return float((self.totalTask - self.tasks.qsize())*self.partSize)/1000.0
+  def getTotalTransfered
+    return float((self.totalTask - self.tasks.qsize())*self.partSize) / 1000.0
   end
     
-  def getProgressRatio(self):
+  def getProgressRatio
     currentQ = float(self.tasks.qsize() - len(self.consumers))
-    return str(float(self.totalTask - currentQ)/self.totalTask)[:6]
+    # NOTE Python sublist [:6] already ported to Ruby [0..5]
+    return str(float(self.totalTask - currentQ) / self.totalTask)[0..5]
   end
 
 end # class MultipartUpload

data/spec/basespaceapi_spec.rb

@@ -14,7 +14,7 @@
 require 'rubygems'
 require 'rspec'
 
-require 'basespace'
+require 'bio-basespace-sdk'
 
 describe Bio::BaseSpace::APIClient do
     describe "initialization" do

data/spec/basespaceerror_spec.rb

@@ -14,7 +14,7 @@
 require 'rubygems'
 require 'rspec'
 
-require 'basespace'
+require 'bio-basespace-sdk'
 
 value = 'testvalue'
 legal = 'legalcases'

data/spec/basespacemodel_spec.rb

@@ -14,7 +14,7 @@
 require 'rubygems'
 require 'rspec'
 
-require 'basespace'
+require 'bio-basespace-sdk'
 
 attributes = { "Id" => "X10231", "Source" => "Test", "SpeciesName" => "Homo sapiens" }
 

metadata

@@ -1,8 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-basespace-sdk
 version: !ruby/object:Gem::Version
-  version: 0.1.2
-  prerelease: 
+  version: 0.1.3
 platform: ruby
 authors:
 - Joachim Baran
@@ -18,71 +17,62 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: getopt
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.4.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.4.1
 - !ruby/object:Gem::Dependency
   name: addressable
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: 2.3.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: 2.3.2
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 2.8.0
+        version: 2.14.1
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 2.8.0
+        version: 2.14.1
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.1.5
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.1.5
 - !ruby/object:Gem::Dependency
   name: jeweler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -90,7 +80,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -98,23 +87,20 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.4.2
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: 1.4.2
 - !ruby/object:Gem::Dependency
   name: rdoc
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -122,20 +108,16 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
         version: '3.12'
-description: ! "Bio::BaseSpace is a Ruby based SDK ported from the Python based BaseSpacePy
-  SDK to be used in the development of Apps and scripts for working with Illumina's
-  BaseSpace cloud-computing solution for next-gen sequencing data analysis.\n\n  The
-  primary purpose of the SDK is to provide an easy-to-use Ruby environment enabling
-  developers to authenticate a user, retrieve data, and upload data/results from their
-  own analysis to BaseSpace.\n\n  If you haven't already done so, you may wish to
-  familiarize yourself with the general BaseSpace developers documentation (https://developer.basespace.illumina.com/)
-  and create a new BaseSpace App to be used when working through the examples provided
-  in 'examples' folder."
+description: |-
+  Bio::BaseSpace is a Ruby based SDK ported from the Python based BaseSpacePy SDK to be used in the development of Apps and scripts for working with Illumina's BaseSpace cloud-computing solution for next-gen sequencing data analysis.
+
+    The primary purpose of the SDK is to provide an easy-to-use Ruby environment enabling developers to authenticate a user, retrieve data, and upload data/results from their own analysis to BaseSpace.
+
+    If you haven't already done so, you may wish to familiarize yourself with the general BaseSpace developers documentation (https://developer.basespace.illumina.com/) and create a new BaseSpace App to be used when working through the examples provided in 'examples' folder.
 email: joachim.baran@gmail.com
 executables: []
 extensions: []
@@ -156,7 +138,6 @@ files:
 - examples/3_accessing_files.rb
 - examples/4_app_result_upload.rb
 - examples/5_purchasing.rb
-- lib/basespace.rb
 - lib/basespace/api/api_client.rb
 - lib/basespace/api/base_api.rb
 - lib/basespace/api/basespace_api.rb
@@ -203,36 +184,33 @@ files:
 - lib/basespace/model/variant_header.rb
 - lib/basespace/model/variant_info.rb
 - lib/basespace/model/variants_header_response.rb
+- lib/bio-basespace-sdk.rb
 - spec/basespaceapi_spec.rb
 - spec/basespaceerror_spec.rb
 - spec/basespacemodel_spec.rb
 homepage: https://github.com/joejimbo/basespace-ruby-sdk
 licenses:
 - Apache, Version 2.0
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
-      segments:
-      - 0
-      hash: -907772599930210264
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.23
+rubygems_version: 2.0.5
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Bio::BaseSpace is a Ruby based SDK to be used in the development of Apps
   and scripts for working with Illumina's BaseSpace cloud-computing solution for next-gen
   sequencing data analysis.