add suport for python3

doc/_update_doc/conf.py

@@ -40,8 +40,8 @@
 master_doc = 'index'
 
 # General information about the project.
-project = u'BaseSpacePy'
-copyright = u'2014, Illumina'
+project = 'BaseSpacePy'
+copyright = '2014, Illumina'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -183,8 +183,8 @@
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-  ('index', 'BaseSpacePy.tex', u'BaseSpacePy Documentation',
-   u'Illumina', 'manual'),
+  ('index', 'BaseSpacePy.tex', 'BaseSpacePy Documentation',
+   'Illumina', 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -213,8 +213,8 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('index', 'basespacepy', u'BaseSpacePy Documentation',
-     [u'Illumina'], 1)
+    ('index', 'basespacepy', 'BaseSpacePy Documentation',
+     ['Illumina'], 1)
 ]
 
 # If true, show URL addresses after external links.
@@ -227,8 +227,8 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  ('index', 'BaseSpacePy', u'BaseSpacePy Documentation',
-   u'Illumina', 'BaseSpacePy', 'One line description of project.',
+  ('index', 'BaseSpacePy', 'BaseSpacePy Documentation',
+   'Illumina', 'BaseSpacePy', 'One line description of project.',
    'Miscellaneous'),
 ]
 

examples/0_Browsing.py

@@ -52,32 +52,32 @@
 
 # First, let's grab the genome with id=4
 myGenome    = myAPI.getGenomeById('4')
-print "\nThe Genome is " + str(myGenome)
-print "We can get more information from the genome object"
-print 'Id: ' + myGenome.Id
-print 'Href: ' + myGenome.Href
-print 'DisplayName: ' + myGenome.DisplayName
+print("\nThe Genome is " + str(myGenome))
+print("We can get more information from the genome object")
+print('Id: ' + myGenome.Id)
+print('Href: ' + myGenome.Href)
+print('DisplayName: ' + myGenome.DisplayName)
 
 # Get a list of all genomes
 allGenomes  = myAPI.getAvailableGenomes()
-print "\nGenomes \n" + str(allGenomes)
+print("\nGenomes \n" + str(allGenomes))
 
 # Let's have a look at the current user
 user        = myAPI.getUserById('current')
-print "\nThe current user is \n" + str(user)
+print("\nThe current user is \n" + str(user))
 
 # Now list the projects for this user
 myProjects   = myAPI.getProjectByUser()
-print "\nThe projects for this user are \n" + str(myProjects)
+print("\nThe projects for this user are \n" + str(myProjects))
 
 # We can also achieve this by making a call using the 'user instance'
 myProjects2 = user.getProjects(myAPI)
-print "\nProjects retrieved from the user instance \n" + str(myProjects2)
+print("\nProjects retrieved from the user instance \n" + str(myProjects2))
 
 # List the runs available for the current user
 runs = user.getRuns(myAPI)
-print "\nThe runs for this user are \n" + str(runs)
+print("\nThe runs for this user are \n" + str(runs))
 
 # In the same manner we can get a list of accessible user runs
 runs = user.getRuns(myAPI)
-print "\nRuns retrieved from user instance \n" + str(runs)
+print("\nRuns retrieved from user instance \n" + str(runs))

examples/1_AccessingFiles.py

@@ -51,40 +51,40 @@
 
 # Let's list all the AppResults and samples for these projects
 for singleProject in myProjects:
-    print "# " + str(singleProject)
+    print("# " + str(singleProject))
     appResults = singleProject.getAppResults(myAPI)
-    print "    The App results for project " + str(singleProject) + " are \n\t" + str(appResults)
+    print("    The App results for project " + str(singleProject) + " are \n\t" + str(appResults))
     samples = singleProject.getSamples(myAPI)
-    print "    The samples for project " + str(singleProject) + " are \n\t" + str(samples)
+    print("    The samples for project " + str(singleProject) + " are \n\t" + str(samples))
 #
 ## we'll take a further look at the files belonging to the sample and 
 ##analyses from the last project in the loop above 
 for a in appResults:
-    print "# " + a.Id
+    print("# " + a.Id)
     ff = a.getFiles(myAPI)
-    print ff
+    print(ff)
 for s in samples:
-    print "Sample " + str(s)
+    print("Sample " + str(s))
     ff = s.getFiles(myAPI)
-    print ff
+    print(ff)
 
 
 ## Now let's do some work with files 
 ## we'll grab a BAM by id and get the coverage for an interval + accompanying meta-data 
 myBam = myAPI.getFileById('9895890')
-print myBam
+print(myBam)
 cov     = myBam.getIntervalCoverage(myAPI,'chr','1','100')
-print cov 
+print(cov) 
 try:
    covMeta = myBam.getCoverageMeta(myAPI,'chr')
 except Exception as e:
-    print "Coverage metadata may not be available for this BAM file: %s" % str(e)
+    print("Coverage metadata may not be available for this BAM file: %s" % str(e))
 else:
-    print covMeta
+    print(covMeta)
 #
 ## and a vcf file
 myVCF = myAPI.getFileById('9895892')
 varMeta = myVCF.getVariantMeta(myAPI)
-print varMeta
+print(varMeta)
 var     = myVCF.filterVariant(myAPI,'chr','1', '25000') 
-print var
+print(var)

examples/2_AppTriggering.py

@@ -51,30 +51,30 @@
 
 # Using the basespaceApi we can request the appSession object corresponding to the AppSession id supplied
 myAppSession = myAPI.getAppSession()
-print myAppSession
+print(myAppSession)
 
 # An app session contains a referal to one or more appLaunchObjects which reference the data module
 # the user launched the app on. This can be a list of projects, samples, or a mixture of objects  
-print "\nType of data the app was triggered on can be seen in 'references'"
-print myAppSession.References
+print("\nType of data the app was triggered on can be seen in 'references'")
+print(myAppSession.References)
 
 # We can also get a handle to the user who started the AppSession
-print "\nWe can get a handle for the user who triggered the app\n" + str(myAppSession.UserCreatedBy)
+print("\nWe can get a handle for the user who triggered the app\n" + str(myAppSession.UserCreatedBy))
 
 # Let's have a closer look at the appSessionLaunchObject
 myReference =  myAppSession.References[0]
-print "\nWe can get out information such as the href to the launch object:"
-print myReference.HrefContent
-print "\nand the specific type of that object:"
-print myReference.Type
+print("\nWe can get out information such as the href to the launch object:")
+print(myReference.HrefContent)
+print("\nand the specific type of that object:")
+print(myReference.Type)
 
 
 # Now we will want to ask for more permission for the specific reference object
-print "\nWe can get out the specific project objects by using 'content':" 
+print("\nWe can get out the specific project objects by using 'content':") 
 myReference =  myReference.Content
-print myReference
-print "\nThe scope string for requesting read access to the reference object is:"
-print myReference.getAccessStr(scope='write')
+print(myReference)
+print("\nThe scope string for requesting read access to the reference object is:")
+print(myReference.getAccessStr(scope='write'))
 
 # We can easily request write access to the reference object so our App can start contributing analysis
 # by default we ask for write permission and authentication for a device

examples/3_Authentication.py

@@ -17,7 +17,7 @@
 from BaseSpacePy.api.BaseSpaceAPI import BaseSpaceAPI
 import time
 import webbrowser 
-import cPickle as Pickle
+import pickle as Pickle
 import os
 
 """
@@ -50,13 +50,13 @@
 
 # First, get the verification code and uri for scope 'browse global'
 deviceInfo = myAPI.getVerificationCode('browse global')
-print "\n URL for user to visit and grant access: "
-print deviceInfo['verification_with_code_uri']
+print("\n URL for user to visit and grant access: ")
+print(deviceInfo['verification_with_code_uri'])
 
 ## PAUSE HERE
 # Have the user visit the verification uri to grant us access
-print "\nPlease visit the uri within 15 seconds and grant access"
-print deviceInfo['verification_with_code_uri']
+print("\nPlease visit the uri within 15 seconds and grant access")
+print(deviceInfo['verification_with_code_uri'])
 webbrowser.open_new(deviceInfo['verification_with_code_uri'])
 time.sleep(15)
 ## PAUSE HERE
@@ -68,22 +68,22 @@
 myAPI.updatePrivileges(code)
 
 # As a reference the provided access-token can be obtained from the BaseSpaceApi object
-print "\nMy Access-token:"
-print myAPI.getAccessToken()
+print("\nMy Access-token:")
+print(myAPI.getAccessToken())
 
 
 # Let's try and grab all available genomes with our new api! 
 allGenomes  = myAPI.getAvailableGenomes()
-print "\nGenomes \n" + str(allGenomes)
+print("\nGenomes \n" + str(allGenomes))
 
 
 # If at a later stage we wish to initialize a BaseSpaceAPI object when we already have
 # an access-token from a previous sessions, this may simply be done by initializing the BaseSpaceAPI
 # object using the key-word AccessToken.
 myToken = myAPI.getAccessToken()
 myAPI.setAccessToken(myToken)
-print "\nA BaseSpaceAPI instance was updated with an access-token: "
-print myAPI 
+print("\nA BaseSpaceAPI instance was updated with an access-token: ")
+print(myAPI) 
 
 #################### Web-based verification #################################
 # The scenario where the authentication is done through a web-browser
@@ -94,8 +94,8 @@
     BSapiWeb = BaseSpaceAPI(profile='DEFAULT')
 userUrl= BSapiWeb.getWebVerificationCode('browse global','http://localhost',state='myState')
 
-print "\nHave the user visit:"
-print userUrl
+print("\nHave the user visit:")
+print(userUrl)
 
 webbrowser.open_new(userUrl)
 
@@ -121,8 +121,8 @@
 
 # Get current user
 user= myAPI.getUserById('current')
-print user
-print myAPI
+print(user)
+print(myAPI)
 
 #### Here some work goes on
 
@@ -136,7 +136,7 @@
 
 # Imagine the current request is done, we will simulate this by deleting the api instance  
 myAPI = None
-print "\nTry printing the removed API, we get: " + str(myAPI)
+print("\nTry printing the removed API, we get: " + str(myAPI))
 
 
 # Next request in the session with id = id123 comes in
@@ -145,10 +145,10 @@
     f = open(mySessionId)
     myAPI = Pickle.load(f)
     f.close()
-    print 
-    print "We got the API back!"
-    print myAPI
+    print() 
+    print("We got the API back!")
+    print(myAPI)
 else:
-    print "Looks like we haven't stored anything for this session yet"
+    print("Looks like we haven't stored anything for this session yet")
     # create a BaseSpaceAPI for the first time
 

examples/4_AppResultUpload.py

@@ -49,41 +49,41 @@
 # Assuming we have write access to the project
 # we will list the current App Results for the project 
 appRes = p.getAppResults(myAPI,statuses=['Running'])
-print "\nThe current running AppResults are \n" + str(appRes)
+print("\nThe current running AppResults are \n" + str(appRes))
 
 # now let's do some work!
 # to create an appResults for a project, simply give the name and description
 appResults = p.createAppResult(myAPI,"testing","this is my results",appSessionId='')
-print "\nSome info about our new app results"
-print appResults
-print appResults.Id
-print "\nThe app results also comes with a reference to our AppSession"
+print("\nSome info about our new app results")
+print(appResults)
+print(appResults.Id)
+print("\nThe app results also comes with a reference to our AppSession")
 myAppSession = appResults.AppSession
-print myAppSession
+print(myAppSession)
 
 # we can change the status of our AppSession and add a status-summary as follows
 myAppSession.setStatus(myAPI,'needsattention',"We worked hard, but encountered some trouble.")
-print "\nAfter a change of status of the app sessions we get\n" + str(myAppSession)
+print("\nAfter a change of status of the app sessions we get\n" + str(myAppSession))
 # we'll set our appSession back to running so we can do some more work
 myAppSession.setStatus(myAPI,'running',"Back on track")
 
 
 ### Let's list all AppResults again and see if our new object shows up 
 appRes = p.getAppResults(myAPI,statuses=['Running'])
-print "\nThe updated app results are \n" + str(appRes)
+print("\nThe updated app results are \n" + str(appRes))
 appResult2 = myAPI.getAppResultById(appResults.Id)
-print appResult2
+print(appResult2)
 
 ## Now we will make another AppResult 
 ## and try to upload a file to it
 appResults2 = p.createAppResult(myAPI,"My second AppResult","This one I will upload to")
 appResults2.uploadFile(myAPI, '/home/mkallberg/Desktop/testFile2.txt', 'BaseSpaceTestFile.txt', '/mydir/', 'text/plain')
-print "\nMy AppResult number 2 \n" + str(appResults2)
+print("\nMy AppResult number 2 \n" + str(appResults2))
 
 ## let's see if our new file made it
 appResultFiles = appResults2.getFiles(myAPI)
-print "\nThese are the files in the appResult"
-print appResultFiles
+print("\nThese are the files in the appResult")
+print(appResultFiles)
 f = appResultFiles[-1]
 
 # we can even download our newly uploaded file