Python 2 and 3 compatibility; Continuous Integration; Static Analysis

.gitignore

@@ -13,3 +13,4 @@ parts
 var
 sdist
 /scripts
+data/BC-12_S12_L001_R2_001.fastq.gz

.travis.yml

@@ -0,0 +1,6 @@
+language: python
+python:
+  - "2.7"
+  - "3.5"
+install: "cd src && python setup.py install && cd .."
+script: ./runtests.sh

README.md

@@ -1,7 +1,11 @@
-INTRODUCTION	
+[![Build Status][travis-image]](https://travis-ci.org/dtenenba/basespace-python-sdk)
+
+[travis-image]: https://img.shields.io/travis/dtenenba/basespace-python-sdk.svg?style=flat&branch=develop
+
+INTRODUCTION
 =========================================
 
-BaseSpacePy is a Python 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. 
+BaseSpacePy is a Python 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.
 
 The primary purpose of the SDK is to provide an easy-to-use Python environment enabling developers to authenticate a user, retrieve data, and upload data/results from their own analysis to BaseSpace.
 
@@ -39,7 +43,7 @@ If you do not have root access, you may use the --prefix to specify the install
 
 	python setup.py install --prefix=/folder/in/my/pythonpath
 
-For more install options type: 
+For more install options type:
 
 	python setup.py --help
 
@@ -53,7 +57,7 @@ or add it to the PYTHONPATH at the top of your Python scripts using BaseSpacePy:
 	sys.path.append('/my/path/basespace-python-sdk/src')
 	import BaseSpacePy
 
-To test that everything is working as expected, launch a Python prompt and try importing 'BaseSpacePy': 
+To test that everything is working as expected, launch a Python prompt and try importing 'BaseSpacePy':
 
 	mkallberg@ubuntu:~/$ python
 	>>> import BaseSpacePy
@@ -115,7 +119,7 @@ Update to support changes in BaseSpace REST specification version v1pre3. Specif
 
 v 0.1
 -----------------------------------------
- 
+
 Initial release of BaseSpacePy
 
 COPYING / LICENSE

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

@@ -5,7 +5,7 @@
 you may not use this file except in compliance with the License.
 You may obtain a copy of the License at
 http://www.apache.org/licenses/LICENSE-2.0
- 
+
     Unless required by applicable law or agreed to in writing, software
 distributed under the License is distributed on an "AS IS" BASIS,
 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -14,11 +14,10 @@
 """
 
 from BaseSpacePy.api.BaseSpaceAPI import BaseSpaceAPI
-import os 
 
 """
 This script demonstrates basic browsing of BaseSpace objects once an access-token
-for global browsing has been obtained. 
+for global browsing has been obtained.
 """
 
 """
@@ -30,8 +29,8 @@
 [DEFAULT]
 name = my new app
 clientKey =
-clientSecret = 
-accessToken = 
+clientSecret =
+accessToken =
 appSessionId =
 apiServer = https://api.cloud-hoth.illumina.com/
 apiVersion = v1pre3
@@ -49,35 +48,35 @@
     myAPI = BaseSpaceAPI(clientKey, clientSecret, apiServer, apiVersion, appSessionId)
 else:
     myAPI = BaseSpaceAPI(profile='DEFAULT')
-    
+
 # 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

@@ -5,7 +5,7 @@
 you may not use this file except in compliance with the License.
 You may obtain a copy of the License at
 http://www.apache.org/licenses/LICENSE-2.0
- 
+
     Unless required by applicable law or agreed to in writing, software
 distributed under the License is distributed on an "AS IS" BASIS,
 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -14,16 +14,15 @@
 """
 
 from BaseSpacePy.api.BaseSpaceAPI import BaseSpaceAPI
-import os
 """
-This script demonstrates how to access Samples and AppResults from a projects and how to work with the available 
-file data for such instances. 
+This script demonstrates how to access Samples and AppResults from a projects and how to work with the available
+file data for such instances.
 """
 
 """
-NOTE: The coverage and variants API calls below require access to a public 
+NOTE: The coverage and variants API calls below require access to a public
 dataset. Before running the example, first go to cloud-hoth.illumina.com,
-login, click on Public Data, select the dataset named 'MiSeq B. cereus demo 
+login, click on Public Data, select the dataset named 'MiSeq B. cereus demo
 data', and click the Import button for the Project named 'BaseSpaceDemo'.
 """
 
@@ -51,40 +50,40 @@
 
 # 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 
+## 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 
+## 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
-var     = myVCF.filterVariant(myAPI,'chr','1', '25000') 
-print var
+print(varMeta)
+var     = myVCF.filterVariant(myAPI,'chr','1', '25000')
+print(var)

examples/2_AppTriggering.py

@@ -5,7 +5,7 @@
 you may not use this file except in compliance with the License.
 You may obtain a copy of the License at
 http://www.apache.org/licenses/LICENSE-2.0
- 
+
     Unless required by applicable law or agreed to in writing, software
 distributed under the License is distributed on an "AS IS" BASIS,
 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -14,11 +14,9 @@
 """
 
 from BaseSpacePy.api.BaseSpaceAPI import BaseSpaceAPI
-import webbrowser
-import time
 
 """
-This script demonstrates how to retrieve the AppSession object produced 
+This script demonstrates how to retrieve the AppSession object produced
 when a user initiates an app. Further it's demonstrated how to automatically
 generate the scope strings to request access to the data object (a project or a sample)
 that the app was triggered to analyze.
@@ -51,52 +49,52 @@
 
 # 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
+# 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)
 
 # 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
 #accessMap       = myAPI.getAccess(myReference,accessType='write')
 # We may limit our request to read access only if that's all that is needed
 #readAccessMaps  = myAPI.getAccess(myReference,accessType='read')
 
-#print "\nWe get the following access map for the write request"
-#print accessMap
+#print("\nWe get the following access map for the write request")
+#print(accessMap)
 
 ## 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 accessMap['verification_with_code_uri']
+#print("\nPlease visit the uri within 15 seconds and grant access")
+#print(accessMap['verification_with_code_uri'])
 #webbrowser.open_new(accessMap['verification_with_code_uri'])
 #time.sleep(15)
 ## PAUSE HERE
 
 # Once the user has granted us the access to the object we requested we can
 # get the basespace access token and start browsing simply by calling updatePriviliges
-# on the baseSpaceApi instance    
+# on the baseSpaceApi instance
 #code = accessMap['device_code']
 #myAPI.updatePrivileges(code)
-#print "\nThe BaseSpaceAPI instance was update with write privileges"
-#print myAPI
+#print("\nThe BaseSpaceAPI instance was update with write privileges")
+#print(myAPI)