def setUp(self):
self.factory = AnalysisFactory()
self.ana = self.factory.createAnalysisFromModuleName("Bowtie2")
self.ana.param = " -x ../testdata/databases/Arabidopsis_TAIR.9.171 "
AnalysisUtils.setInputFiles(self.ana,
["../testdata/FoxP2_SL167.fastq"],
['fastq'])
self.ana.init()
def setUp(self):
self.input = []
self.input.append("testdata/FoxP2_SL167.fastq")
self.analysis = AnalysisFactory.createAnalysisFromModuleName("FastQC")
self.analysis.setInputFiles(self.input, ['fastq'])
def testRun(self):
self.ana = AnalysisFactory.createAnalysisFromModuleName("FastQC")
self.ana.setInputFiles(self.input_files, self.input_types)
self.assertTrue(len(self.input_files) == 1)
self.assertTrue(len(self.input_types) == 1)
cmds = self.ana.getCommands()
print cmds
self.assertTrue(len(cmds) == 1)
runner = AnalysisRunner(self.ana)
res = runner.run()
self.assertTrue(res)
self.ana.postProcessOutput()
output_str = self.ana.output_str
self.assertTrue(len(output_str) == 4)
def testRun(self):
self.ana = AnalysisFactory.createAnalysisFromModuleName(
"ParallelMpileup")
self.ana.setInputFiles(self.input_files, self.input_types)
self.ana.refgenome = self.refgenome
self.assertTrue(len(self.input_files) == 1)
self.assertTrue(len(self.input_types) == 1)
self.ana.init()
cmds = self.ana.getCommands()
print cmds
self.assertTrue(len(cmds) == 2)
runner = AnalysisRunner(self.ana)
res = runner.run()
self.assertTrue(res)
self.ana.postProcessOutput()
output_strings = self.ana.output_strings
print output_strings
for strobj in output_strings:
print strobj.output_string
self.assertTrue(len(output_strings) == 2)
def setUp(self):
self.ana = AnalysisFactory.createAnalysisFromModuleName("FastQC")
self.ana.setInputFiles(["../testdata/FoxP2_SL167.fastq"], ['fastq'])
print "Input %s" % self.ana.input_files
self.db = AnalysisDBFactory(settings.TESTDBNAME)
def createAnalysisRunnerClass(self):
print self.args
self.dbfactory = AnalysisDBFactory(settings.DBNAME)
self.ana = AnalysisFactory.createAnalysisFromModuleName(self.args.analysis)
self.ana.setInputFiles (self.args.input,self.args.input_type)
self.ana.init()
self.ana.setParameters (self.args.param)
self.dbfactory.saveAnalysis(self.ana)
def getCommands(self):
self.commands = []
self.output_files = []
self.checkDiskSpace()
print "Reading genome file"
seqs = FastaFile.getSequenceDict(self.refgenome,False)
if self.checkInputFiles() == False:
raise Exception("Input files [%s] don't exist = can't continue"%(self.input_files))
fileparts = FileUtils.getFileParts(self.input_files[0])
self.basename = fileparts['basename']
for seq in seqs:
len = seqs[seq]['len']
i = 1
while i < len:
end = i + self.chunk -1
if end > len:
end = len
regionstr = "%s:%d-%d"%(seq,i,end)
tmpana = AnalysisFactory.createAnalysisFromModuleName("SamtoolsMpileup")
tmpana.setInputFiles(self.input_files,self.input_types)
tmpana.refgenome = self.refgenome
tmpana.regionstr = regionstr
tmpana.init()
tmpcmds = tmpana.getCommands()
for cmd in tmpcmds:
self.commands.append(cmd)
i = i + self.chunk
return self.commands
class ObjectCreateCheck(unittest.TestCase
): # Class with unitttest.TestCase as arg -
def setUp(self):
self.factory = AnalysisFactory()
self.ana = self.factory.createAnalysisFromModuleName("Bowtie2")
self.ana.param = " -x ../testdata/databases/Arabidopsis_TAIR.9.171 "
AnalysisUtils.setInputFiles(self.ana,
["../testdata/FoxP2_SL167.fastq"],
['fastq'])
self.ana.init()
def testCreateNewAnalysisRunner(
self): # Function gets called automatically
"""New instance should create successfully"""
anarun = AnalysisRunner(self.ana)
tmpinputs = AnalysisUtils.getInputFiles(anarun.analysis)
self.assertTrue(anarun)
def testRun(self):
anarun = AnalysisRunner(self.ana)
res = anarun.run()
self.assertTrue(res)
def testGetOutput(self):
anarun = AnalysisRunner(self.ana)
res = anarun.run()
anarun.analysis.postProcessOutput()
out = anarun.analysis.output_files
print out
print anarun.analysis.summary_data
self.assertTrue(len(out) == 2)
def fetchAnalysisByID(self, id):
logging.info(" ========> AnalysisDB Fetching analysis by id : %s" % id)
try:
sql = "select * from Analysis where ID = %s" % id
cur = self.executeQuery(sql)
rows = cur.fetchall()
if (len(rows) == 1):
row = rows[0]
name = row[1]
ana = AnalysisFactory.createAnalysisFromModuleName(name)
ana.id = id
ana.owner = row[2]
ana.owner_email = row[3]
ana.current_status = row[4]
ana.output_status = row[5]
ana.input_dir = row[6]
ana.working_dir = row[7]
ana.output_dir = row[8]
ana.runtype = row[9]
ana.param = row[10]
ana.queue = row[11]
ana.slurmid = row[12]
ana.cores = row[13]
ana.mempercore = row[14]
ana.last_updated = row[15]
ana.date_created = row[16]
# Get the data from the linked tables
tables = [
'InputFile', 'ExpectedOutputFile', 'OutputFile', 'Command',
'SlurmValue', 'SummaryValue', 'Status'
]
for t in tables:
tmpstr = "Analysis" + t
query = "select * from %s where AnalysisID=%d" % (tmpstr,
id)
cur = self.executeQuery(query)
rows = cur.fetchall()
for r in rows:
if t == "Command":
ana.commands.append(r[2])
if t == "InputFile":
ana.input_files.append(r[2])
ana.input_types.append(r[3])
if t == "ExpectedOutputFile":
ana.expected_output_files.append(r[2])
if t == "OutputFile":
ana.output_files.append(r[2])
ana.output_types.append(r[3])
if t == "SlurmValue":
ana.slurmparams[r[2]] = r[3]
if t == "SummaryValue":
ana.summary_data[r[2]] = r[3]
elif (len(rows) == 0):
return None
elif len(rows) > 1:
logging.error(
" ========> AnalysisDB Error fetching analysis. Non unique id %d : %s"
% (id, e.args[0]))
raise Exception(
"ERROR: analysis id should be unique - multiple rows returned. id is [%d]"
% id)
ana.init()
print ana.toString()
return ana
except sqlite3.Error, e:
if self.con:
self.con.rollback()
logging.error(
" ========> AnalysisDB Error fetching analysis id %d : %s"
% (id, e.args[0]))
raise
def toString(self):
return AnalysisFactory.toString(self)
def setUp(self):
self.dbobj = AnalysisDBFactory(settings.TESTDBNAME)
self.ana_fact = AnalysisFactory()
self.anaobj = self.ana_fact.createAnalysisFromModuleName("FastQC")
self.anaobj.setInputFiles(["../testdata/FoxP2_SL167.fastq"], ['fastq'])
class ObjectCreateCheck(unittest.TestCase
): # Class with unitttest.TestCase as arg -
def setUp(self):
self.dbobj = AnalysisDBFactory(settings.TESTDBNAME)
self.ana_fact = AnalysisFactory()
self.anaobj = self.ana_fact.createAnalysisFromModuleName("FastQC")
self.anaobj.setInputFiles(["../testdata/FoxP2_SL167.fastq"], ['fastq'])
def testCreateObject(self):
""" Test we can create a new AnalysisDBFactory object """
self.assertTrue(self.dbobj)
def testCreateAnalysisTables(self):
""" Test we can create the Analysis tables """
self.assertTrue(self.dbobj.createAnalysisTables())
def testGetTables(self):
""" Test we can retrive a list of db tables """
self.dbobj.createAnalysisTables()
rows = self.dbobj.getTables()
self.assertTrue(len(rows) == 9)
def testAddAnalysisToDB(self):
""" Test we can save an Analysis object to the DB """
#self.dbobj.createAnalysisTables()
#self.dbobj.saveAnalysis(self.anaobj)
#self.assertTrue(1)
def testFetchAnalsyisFromDB(self):
""" Test we can fetch an existing analysis object from the DB"""
#self.anaobj.id = None
#self.dbobj.saveAnalysis(self.anaobj)
#ana = self.dbobj.fetchAnalysisByID(self.anaobj.id)
#str1 = self.anaobj.toString()
#str2 = ana.toString()
#self.assertTrue(str1 == str2)
def testUpdateAnalysisStatus(self):
""" Test updating an analysis objects status"""
self.anaobj.id = None
self.dbobj.saveAnalysis(self.anaobj)
self.dbobj.updateAnalysisStatus(self.anaobj, "RUNNING")
ana = self.dbobj.fetchAnalysisByID(self.anaobj.id)
str1 = self.anaobj.toString()
str2 = ana.toString()
print "STR1 %s" % str1
print "STR2 %s" % str2
self.assertTrue(ana.current_status == "RUNNING")