Exemple #1
0
 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)
Exemple #2
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 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)                
Exemple #3
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 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/')
Exemple #6
0
        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/")
Exemple #9
0
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/')