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some unit tests pass in py3 (all still pass in py2)
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Lines changed: 1446 additions & 1416 deletions

‎.travis.yml‎

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language: python
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python:
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- "2.7"
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- "3.5"
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install: "cd src && python setup.py install && cd .."
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script: ./runtests.sh

‎doc/_update_doc/conf.py‎

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master_doc = 'index'
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# General information about the project.
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project = u'BaseSpacePy'
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copyright = u'2014, Illumina'
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project = 'BaseSpacePy'
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copyright = '2014, Illumina'
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# The version info for the project you're documenting, acts as replacement for
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# |version| and |release|, also used in various other places throughout the
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# Grouping the document tree into LaTeX files. List of tuples
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# (source start file, target name, title, author, documentclass [howto/manual]).
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latex_documents = [
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('index', 'BaseSpacePy.tex', u'BaseSpacePy Documentation',
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u'Illumina', 'manual'),
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('index', 'BaseSpacePy.tex', 'BaseSpacePy Documentation',
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'Illumina', 'manual'),
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]
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# The name of an image file (relative to this directory) to place at the top of
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# One entry per manual page. List of tuples
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# (source start file, name, description, authors, manual section).
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man_pages = [
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('index', 'basespacepy', u'BaseSpacePy Documentation',
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[u'Illumina'], 1)
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('index', 'basespacepy', 'BaseSpacePy Documentation',
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['Illumina'], 1)
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]
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# If true, show URL addresses after external links.
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# (source start file, target name, title, author,
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# dir menu entry, description, category)
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texinfo_documents = [
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('index', 'BaseSpacePy', u'BaseSpacePy Documentation',
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u'Illumina', 'BaseSpacePy', 'One line description of project.',
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('index', 'BaseSpacePy', 'BaseSpacePy Documentation',
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'Illumina', 'BaseSpacePy', 'One line description of project.',
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'Miscellaneous'),
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]
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‎examples/0_Browsing.py‎

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you may not use this file except in compliance with the License.
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You may obtain a copy of the License at
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http://www.apache.org/licenses/LICENSE-2.0
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Unless required by applicable law or agreed to in writing, software
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distributed under the License is distributed on an "AS IS" BASIS,
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WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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"""
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from BaseSpacePy.api.BaseSpaceAPI import BaseSpaceAPI
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import os
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import os
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"""
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This script demonstrates basic browsing of BaseSpace objects once an access-token
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for global browsing has been obtained.
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for global browsing has been obtained.
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"""
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"""
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[DEFAULT]
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name = my new app
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clientKey =
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clientSecret =
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accessToken =
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clientSecret =
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accessToken =
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appSessionId =
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apiServer = https://api.cloud-hoth.illumina.com/
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apiVersion = v1pre3
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myAPI = BaseSpaceAPI(clientKey, clientSecret, apiServer, apiVersion, appSessionId)
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else:
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myAPI = BaseSpaceAPI(profile='DEFAULT')
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# First, let's grab the genome with id=4
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myGenome = myAPI.getGenomeById('4')
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print "\nThe Genome is " + str(myGenome)
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print "We can get more information from the genome object"
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print 'Id: ' + myGenome.Id
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print 'Href: ' + myGenome.Href
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print 'DisplayName: ' + myGenome.DisplayName
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print("\nThe Genome is " + str(myGenome))
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print("We can get more information from the genome object")
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print('Id: ' + myGenome.Id)
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print('Href: ' + myGenome.Href)
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print('DisplayName: ' + myGenome.DisplayName)
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# Get a list of all genomes
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allGenomes = myAPI.getAvailableGenomes()
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print "\nGenomes \n" + str(allGenomes)
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print("\nGenomes \n" + str(allGenomes))
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# Let's have a look at the current user
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user = myAPI.getUserById('current')
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print "\nThe current user is \n" + str(user)
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print("\nThe current user is \n" + str(user))
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# Now list the projects for this user
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myProjects = myAPI.getProjectByUser()
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print "\nThe projects for this user are \n" + str(myProjects)
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print("\nThe projects for this user are \n" + str(myProjects))
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# We can also achieve this by making a call using the 'user instance'
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myProjects2 = user.getProjects(myAPI)
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print "\nProjects retrieved from the user instance \n" + str(myProjects2)
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print("\nProjects retrieved from the user instance \n" + str(myProjects2))
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# List the runs available for the current user
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runs = user.getRuns(myAPI)
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print "\nThe runs for this user are \n" + str(runs)
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print("\nThe runs for this user are \n" + str(runs))
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# In the same manner we can get a list of accessible user runs
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runs = user.getRuns(myAPI)
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print "\nRuns retrieved from user instance \n" + str(runs)
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print("\nRuns retrieved from user instance \n" + str(runs))

‎examples/1_AccessingFiles.py‎

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you may not use this file except in compliance with the License.
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You may obtain a copy of the License at
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http://www.apache.org/licenses/LICENSE-2.0
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Unless required by applicable law or agreed to in writing, software
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distributed under the License is distributed on an "AS IS" BASIS,
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WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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from BaseSpacePy.api.BaseSpaceAPI import BaseSpaceAPI
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import os
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"""
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This script demonstrates how to access Samples and AppResults from a projects and how to work with the available
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file data for such instances.
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This script demonstrates how to access Samples and AppResults from a projects and how to work with the available
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file data for such instances.
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"""
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"""
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NOTE: The coverage and variants API calls below require access to a public
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NOTE: The coverage and variants API calls below require access to a public
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dataset. Before running the example, first go to cloud-hoth.illumina.com,
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login, click on Public Data, select the dataset named 'MiSeq B. cereus demo
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login, click on Public Data, select the dataset named 'MiSeq B. cereus demo
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data', and click the Import button for the Project named 'BaseSpaceDemo'.
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"""
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# Let's list all the AppResults and samples for these projects
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for singleProject in myProjects:
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print "# " + str(singleProject)
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print("# " + str(singleProject))
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appResults = singleProject.getAppResults(myAPI)
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print " The App results for project " + str(singleProject) + " are \n\t" + str(appResults)
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print(" The App results for project " + str(singleProject) + " are \n\t" + str(appResults))
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samples = singleProject.getSamples(myAPI)
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print " The samples for project " + str(singleProject) + " are \n\t" + str(samples)
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print(" The samples for project " + str(singleProject) + " are \n\t" + str(samples))
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#
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## we'll take a further look at the files belonging to the sample and
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##analyses from the last project in the loop above
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## we'll take a further look at the files belonging to the sample and
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##analyses from the last project in the loop above
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for a in appResults:
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print "# " + a.Id
63+
print("# " + a.Id)
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ff = a.getFiles(myAPI)
65-
print ff
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print(ff)
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for s in samples:
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print "Sample " + str(s)
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print("Sample " + str(s))
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ff = s.getFiles(myAPI)
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print ff
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print(ff)
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72-
## Now let's do some work with files
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## we'll grab a BAM by id and get the coverage for an interval + accompanying meta-data
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## Now let's do some work with files
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## we'll grab a BAM by id and get the coverage for an interval + accompanying meta-data
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myBam = myAPI.getFileById('9895890')
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print myBam
75+
print(myBam)
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cov = myBam.getIntervalCoverage(myAPI,'chr','1','100')
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print cov
77+
print(cov)
7878
try:
7979
covMeta = myBam.getCoverageMeta(myAPI,'chr')
8080
except Exception as e:
81-
print "Coverage metadata may not be available for this BAM file: %s" % str(e)
81+
print("Coverage metadata may not be available for this BAM file: %s" % str(e))
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else:
83-
print covMeta
83+
print(covMeta)
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#
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## and a vcf file
8686
myVCF = myAPI.getFileById('9895892')
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varMeta = myVCF.getVariantMeta(myAPI)
88-
print varMeta
89-
var = myVCF.filterVariant(myAPI,'chr','1', '25000')
90-
print var
88+
print(varMeta)
89+
var = myVCF.filterVariant(myAPI,'chr','1', '25000')
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print(var)

‎examples/2_AppTriggering.py‎

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you may not use this file except in compliance with the License.
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You may obtain a copy of the License at
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http://www.apache.org/licenses/LICENSE-2.0
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Unless required by applicable law or agreed to in writing, software
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distributed under the License is distributed on an "AS IS" BASIS,
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WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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import time
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2020
"""
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This script demonstrates how to retrieve the AppSession object produced
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This script demonstrates how to retrieve the AppSession object produced
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when a user initiates an app. Further it's demonstrated how to automatically
2323
generate the scope strings to request access to the data object (a project or a sample)
2424
that the app was triggered to analyze.
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5252
# Using the basespaceApi we can request the appSession object corresponding to the AppSession id supplied
5353
myAppSession = myAPI.getAppSession()
54-
print myAppSession
54+
print(myAppSession)
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5656
# An app session contains a referal to one or more appLaunchObjects which reference the data module
57-
# the user launched the app on. This can be a list of projects, samples, or a mixture of objects
58-
print "\nType of data the app was triggered on can be seen in 'references'"
59-
print myAppSession.References
57+
# the user launched the app on. This can be a list of projects, samples, or a mixture of objects
58+
print("\nType of data the app was triggered on can be seen in 'references'")
59+
print(myAppSession.References)
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6161
# We can also get a handle to the user who started the AppSession
62-
print "\nWe can get a handle for the user who triggered the app\n" + str(myAppSession.UserCreatedBy)
62+
print("\nWe can get a handle for the user who triggered the app\n" + str(myAppSession.UserCreatedBy))
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6464
# Let's have a closer look at the appSessionLaunchObject
6565
myReference = myAppSession.References[0]
66-
print "\nWe can get out information such as the href to the launch object:"
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print myReference.HrefContent
68-
print "\nand the specific type of that object:"
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print myReference.Type
66+
print("\nWe can get out information such as the href to the launch object:")
67+
print(myReference.HrefContent)
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print("\nand the specific type of that object:")
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print(myReference.Type)
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7272
# Now we will want to ask for more permission for the specific reference object
73-
print "\nWe can get out the specific project objects by using 'content':"
73+
print("\nWe can get out the specific project objects by using 'content':")
7474
myReference = myReference.Content
75-
print myReference
76-
print "\nThe scope string for requesting read access to the reference object is:"
77-
print myReference.getAccessStr(scope='write')
75+
print(myReference)
76+
print("\nThe scope string for requesting read access to the reference object is:")
77+
print(myReference.getAccessStr(scope='write'))
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7979
# We can easily request write access to the reference object so our App can start contributing analysis
8080
# by default we ask for write permission and authentication for a device
8181
#accessMap = myAPI.getAccess(myReference,accessType='write')
8282
# We may limit our request to read access only if that's all that is needed
8383
#readAccessMaps = myAPI.getAccess(myReference,accessType='read')
8484

85-
#print "\nWe get the following access map for the write request"
86-
#print accessMap
85+
#print("\nWe get the following access map for the write request")
86+
#print(accessMap)
8787

8888
## PAUSE HERE
8989
# Have the user visit the verification uri to grant us access
90-
#print "\nPlease visit the uri within 15 seconds and grant access"
91-
#print accessMap['verification_with_code_uri']
90+
#print("\nPlease visit the uri within 15 seconds and grant access")
91+
#print(accessMap['verification_with_code_uri'])
9292
#webbrowser.open_new(accessMap['verification_with_code_uri'])
9393
#time.sleep(15)
9494
## PAUSE HERE
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9696
# Once the user has granted us the access to the object we requested we can
9797
# get the basespace access token and start browsing simply by calling updatePriviliges
98-
# on the baseSpaceApi instance
98+
# on the baseSpaceApi instance
9999
#code = accessMap['device_code']
100100
#myAPI.updatePrivileges(code)
101-
#print "\nThe BaseSpaceAPI instance was update with write privileges"
102-
#print myAPI
101+
#print("\nThe BaseSpaceAPI instance was update with write privileges")
102+
#print(myAPI)

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