def calc_quantity(self, file_num, user_id, live_purchase):
"""
Calculates quantity of product needed to purchase from analyzing the provided file
If live_purchase is True, free trials are decremented from the db
"""
db=current.db
self.file_num = file_num
self.free_trial = False
if(self.prod_name == current.product_names['AlignmentQC']):
user_row = db(db.auth_user.id==user_id).select().first()
app = db(db.app_data.id > 0).select().first()
bs_api = BaseSpaceAPI(app.client_id, app.client_secret, app.baseSpaceUrl, app.version, "", user_row.access_token)
input_file = bs_api.getFileById(file_num)
# BAM files less than 100 MB are free
if input_file.Size < 100*(2**20):
self.prod_quantity = 0
else:
# determine if free trial
trial_row = db((db.free_trial.user_id==user_row.id) &
(db.free_trial.product_id==self.prod_id) &
(db.free_trial.trials > 0)).select().first()
if trial_row:
# decrement trials in db
if live_purchase:
trial_row.update_record(trials=int(trial_row.trials) - 1)
self.prod_quantity = 0
self.free_trial = True
else:
self.prod_quantity = 1
else:
raise UnrecognizedProductException(self.prod_name)
def get_file_url(self, file_num, app_session_id):
"""
Returns the S3 link to the provided file
"""
db = current.db
# get access token for app session's user (can't use current user since may be accessing from scheduler worker)
ssn_row = db(db.app_session.id==app_session_id).select().first()
user_row = db(db.auth_user.id==ssn_row.user_id).select().first()
app = db(db.app_data.id > 0).select().first()
bs_api = BaseSpaceAPI(app.client_id, app.client_secret, app.baseSpaceUrl, app.version, ssn_row.app_session_num, user_row.access_token)
f = bs_api.getFileById(file_num)
return f.getFileUrl(bs_api)
def download_file(self, file_num, local_dir, app_session_id):
"""
Download a file from BaseSpace into the provided directory (created if doesn't exist)
"""
db = current.db
# get access token for app session's user (can't use current user since may be accessing from scheduler worker)
ssn_row = db(db.app_session.id==app_session_id).select().first()
user_row = db(db.auth_user.id==ssn_row.user_id).select().first()
# get file info from BaseSpace
app = db(db.app_data.id > 0).select().first()
bs_api = BaseSpaceAPI(app.client_id, app.client_secret, app.baseSpaceUrl, app.version, ssn_row.app_session_num, user_row.access_token)
f = bs_api.getFileById(file_num)
# create local_path dir if it doesn't exist
if not os.path.exists(local_dir):
os.makedirs(local_dir)
# write downloaded data to new file
f.downloadFile(bs_api,local_dir)
self.local_path = os.path.join(local_dir, f.Name)
samples = singleProject.getSamples(myAPI)
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
ff = a.getFiles(myAPI)
print ff
for s in samples:
print "Sample " + str(s)
ff = s.getFiles(myAPI)
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('2150156')
print myBam
cov = myBam.getIntervalCoverage(myAPI,'chr2','1','20000')
print cov
covMeta = myBam.getCoverageMeta(myAPI,'chr2')
print covMeta
#
## and a vcf file
myVCF = myAPI.getFileById('2150158')
##Let's get the variant meta info
varMeta = myVCF.getVariantMeta(myAPI)
print varMeta
var = myVCF.filterVariant(myAPI,'2','1', '11000')
print var
myAppSession = appResults.AppSession print myAppSession # we can change the status of our AppSession and add a status-summary as follows myAppSession.setStatus(myBaseSpaceAPI,'needsattention',"We worked hard, but encountered some trouble.") 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(myBaseSpaceAPI,'running',"Back on track") ### Let's list all AppResults again and see if our new object shows up appRes = p.getAppResults(myBaseSpaceAPI,statuses=['Running']) print "\nThe updated app results are \n" + str(appRes) appResult2 = myBaseSpaceAPI.getAppResultById(appResults.Id) print appResult2 ## Now we will make another AppResult ## and try to upload a file to it appResults2 = p.createAppResult(myBaseSpaceAPI,"My second AppResult","This one I will upload to") appResults2.uploadFile(myBaseSpaceAPI, '/home/mkallberg/Desktop/testFile2.txt', 'BaseSpaceTestFile.txt', '/mydir/', 'text/plain') print "\nMy AppResult number 2 \n" + str(appResults2) ## let's see if our new file made it appResultFiles = appResults2.getFiles(myBaseSpaceAPI) print "\nThese are the files in the appResult" print appResultFiles f = appResultFiles[-1] # we can even download our newly uploaded file f = myBaseSpaceAPI.getFileById(f.Id) f.downloadFile(myBaseSpaceAPI,'/home/mkallberg/Desktop/')
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
ff = a.getFiles(myAPI)
print ff
for s in samples:
print "Sample " + str(s)
ff = s.getFiles(myAPI)
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
cov = myBam.getIntervalCoverage(myAPI, 'chr', '1', '100')
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)
else:
print covMeta
#
## and a vcf file
myVCF = myAPI.getFileById('9895892')
varMeta = myVCF.getVariantMeta(myAPI)
print varMeta
#
## 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
ff = a.getFiles(myAPI)
print ff
for s in samples:
print "Sample " + str(s)
ff = s.getFiles(myAPI)
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
cov = myBam.getIntervalCoverage(myAPI,'chr','1','100')
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)
else:
print covMeta
#
## and a vcf file
myVCF = myAPI.getFileById('9895892')
varMeta = myVCF.getVariantMeta(myAPI)
print varMeta
var = myVCF.filterVariant(myAPI,'chr','1', '25000')
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) # 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) appResult2 = myAPI.getAppResultById(appResults.Id) 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) ## let's see if our new file made it appResultFiles = appResults2.getFiles(myAPI) print "\nThese are the files in the appResult" print appResultFiles f = appResultFiles[-1] # we can even download our newly uploaded file f = myAPI.getFileById(f.Id) f.downloadFile(myAPI, "/home/mkallberg/Desktop/")
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))
# 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))
appResult2 = myAPI.getAppResultById(appResults.Id)
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))
## let's see if our new file made it
appResultFiles = appResults2.getFiles(myAPI)
print("\nThese are the files in the appResult")
print(appResultFiles)
f = appResultFiles[-1]
# we can even download our newly uploaded file
f = myAPI.getFileById(f.Id)
f.downloadFile(myAPI, '/home/mkallberg/Desktop/')
