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convert has_key to X in dictionary
author
Diane Trout
<diane@ghic.org>
Thu, 29 Jan 2015 21:59:07 +0000
(13:59 -0800)
committer
Diane Trout
<diane@ghic.org>
Thu, 29 Jan 2015 21:59:07 +0000
(13:59 -0800)
experiments/experiments.py
patch
|
blob
|
history
htsworkflow/auth.py
patch
|
blob
|
history
htsworkflow/automation/spoolwatcher.py
patch
|
blob
|
history
htsworkflow/frontend/analysis/main.py
patch
|
blob
|
history
htsworkflow/frontend/reports/reports.py
patch
|
blob
|
history
htsworkflow/pipelines/bustard.py
patch
|
blob
|
history
htsworkflow/pipelines/ipar.py
patch
|
blob
|
history
htsworkflow/pipelines/summary.py
patch
|
blob
|
history
htsworkflow/util/fctracker.py
patch
|
blob
|
history
scripts/htsw-update-archive
patch
|
blob
|
history
diff --git
a/experiments/experiments.py
b/experiments/experiments.py
index b8f905ecf3682d0e59e340b4597c12a17fdc084d..8738224d547ea47693902a2f48bf25c7affd526f 100644
(file)
--- a/
experiments/experiments.py
+++ b/
experiments/experiments.py
@@
-148,22
+148,22
@@
def updStatus(request):
user = request.user
#Check access permission
user = request.user
#Check access permission
- if not (user.is_superuser and
settings.ALLOWED_IPS.has_key(ClIP)
):
+ if not (user.is_superuser and
ClIP in settings.ALLOWED_IPS
):
return HttpResponse("%s access denied from %s." % (user, ClIP))
# ~~~~~~Parameters for the job ~~~~
return HttpResponse("%s access denied from %s." % (user, ClIP))
# ~~~~~~Parameters for the job ~~~~
- if
request.REQUEST.has_key('fcid')
:
+ if
'fcid' in request.REQUEST
:
fcid = request.REQUEST['fcid']
else:
return HttpResponse('missing fcid')
fcid = request.REQUEST['fcid']
else:
return HttpResponse('missing fcid')
- if
request.REQUEST.has_key('runf')
:
+ if
'runf' in request.REQUEST
:
runfolder = request.REQUEST['runf']
else:
return HttpResponse('missing runf')
runfolder = request.REQUEST['runf']
else:
return HttpResponse('missing runf')
- if
request.REQUEST.has_key('updst')
:
+ if
'updst' in request.REQUEST
:
UpdatedStatus = request.REQUEST['updst']
else:
return HttpResponse('missing status')
UpdatedStatus = request.REQUEST['updst']
else:
return HttpResponse('missing status')
@@
-179,7
+179,7
@@
def updStatus(request):
#if there's a message update that too
mytimestamp = timezone.now().__str__()
mytimestamp = re.sub(pattern=":[^:]*$",repl="",string=mytimestamp)
#if there's a message update that too
mytimestamp = timezone.now().__str__()
mytimestamp = re.sub(pattern=":[^:]*$",repl="",string=mytimestamp)
- if
request.REQUEST.has_key('msg')
:
+ if
'msg' in request.REQUEST
:
rec.run_note += ", "+request.REQUEST['msg']+" ("+mytimestamp+")"
else :
if UpdatedStatus == '1':
rec.run_note += ", "+request.REQUEST['msg']+" ("+mytimestamp+")"
else :
if UpdatedStatus == '1':
@@
-201,7
+201,7
@@
def updStatus(request):
def generateConfile(request,fcid):
#granted = False
#ClIP = request.META['REMOTE_ADDR']
def generateConfile(request,fcid):
#granted = False
#ClIP = request.META['REMOTE_ADDR']
- #if (
settings.ALLOWED_IPS.has_key(ClIP)
): granted = True
+ #if (
ClIP in settings.ALLOWED_IPS
): granted = True
#if not granted: return HttpResponse("access denied.")
#if not granted: return HttpResponse("access denied.")
@@
-228,7
+228,7
@@
def generateConfile(request,fcid):
def getConfile(req):
granted = False
ClIP = req.META['REMOTE_ADDR']
def getConfile(req):
granted = False
ClIP = req.META['REMOTE_ADDR']
- if (
settings.ALLOWED_IPS.has_key(ClIP)
): granted = True
+ if (
ClIP in settings.ALLOWED_IPS
): granted = True
if not granted: return HttpResponse("access denied. IP: "+ClIP)
if not granted: return HttpResponse("access denied. IP: "+ClIP)
@@
-236,9
+236,9
@@
def getConfile(req):
cnfgfile = 'Nothing found'
runfolder = 'unknown'
request = req.REQUEST
cnfgfile = 'Nothing found'
runfolder = 'unknown'
request = req.REQUEST
- if
request.has_key('fcid')
:
+ if
'fcid' in request
:
fcid = request['fcid']
fcid = request['fcid']
- if
request.has_key('runf')
:
+ if
'runf' in request
:
runfolder = request['runf']
try:
rec = DataRun.objects.get(run_folder=runfolder) #,flowcell_id=fcid)
runfolder = request['runf']
try:
rec = DataRun.objects.get(run_folder=runfolder) #,flowcell_id=fcid)
@@
-262,14
+262,14
@@
def getConfile(req):
def getLaneLibs(req):
granted = False
ClIP = req.META['REMOTE_ADDR']
def getLaneLibs(req):
granted = False
ClIP = req.META['REMOTE_ADDR']
- if (
settings.ALLOWED_IPS.has_key(ClIP)
): granted = True
+ if (
ClIP in settings.ALLOWED_IPS
): granted = True
if not granted: return HttpResponse("access denied.")
request = req.REQUEST
fcid = 'none'
outputfile = ''
if not granted: return HttpResponse("access denied.")
request = req.REQUEST
fcid = 'none'
outputfile = ''
- if
request.has_key('fcid')
:
+ if
'fcid' in request
:
fcid = request['fcid']
try:
rec = FlowCell.objects.get(flowcell_id=fcid)
fcid = request['fcid']
try:
rec = FlowCell.objects.get(flowcell_id=fcid)
diff --git
a/htsworkflow/auth.py
b/htsworkflow/auth.py
index 5688cc9c061231c560ade2fe0b694e238193dc82..1d781e19c3a44dda03bd9aacf4c5201a7010945e 100644
(file)
--- a/
htsworkflow/auth.py
+++ b/
htsworkflow/auth.py
@@
-8,7
+8,7
@@
apidata = {'apiid': u'0', 'apikey': settings.DEFAULT_API_KEY}
def require_api_key(request):
# make sure we have the api component
def require_api_key(request):
# make sure we have the api component
- if not (
request.REQUEST.has_key('apiid') or request.REQUEST.has_key('apikey')
):
+ if not (
'apiid' in request.REQUEST or 'apikey' in request.REQUEST
):
raise PermissionDenied
# make sure the id and key are right
raise PermissionDenied
# make sure the id and key are right
diff --git
a/htsworkflow/automation/spoolwatcher.py
b/htsworkflow/automation/spoolwatcher.py
index e226234d6d392f67cd774cb436dc9660ad22e71b..2888be0beaac1d1e46ee0af34b8114ba2c4ecc76 100644
(file)
--- a/
htsworkflow/automation/spoolwatcher.py
+++ b/
htsworkflow/automation/spoolwatcher.py
@@
-72,7
+72,7
@@
class Handler(pyinotify.ProcessEvent):
# if we've already seen an event in this directory (AKA runfolder)
# keep track if its already hit the "completed" flag
# if we've already seen an event in this directory (AKA runfolder)
# keep track if its already hit the "completed" flag
- if
watch_path_events.has_key(target)
:
+ if
target in watch_path_events
:
run_already_complete = watch_path_events[target].complete
watch_path_events[target] = WatcherEvent(target)
run_already_complete = watch_path_events[target].complete
watch_path_events[target] = WatcherEvent(target)
diff --git
a/htsworkflow/frontend/analysis/main.py
b/htsworkflow/frontend/analysis/main.py
index ba2a739d5be0b461aaf02264a40dda6ed90e6863..71d711d72dca7e9dac47806e9b3e4635d842d123 100644
(file)
--- a/
htsworkflow/frontend/analysis/main.py
+++ b/
htsworkflow/frontend/analysis/main.py
@@
-14,20
+14,20
@@
def updStatus(request):
ClIP = request.META['REMOTE_ADDR']
#Check client access permission
granted = False
ClIP = request.META['REMOTE_ADDR']
#Check client access permission
granted = False
- if (
settings.ALLOWED_ANALYS_IPS.has_key(ClIP)
): granted = True
+ if (
ClIP in settings.ALLOWED_ANALYS_IPS
): granted = True
if not granted: return HttpResponse("access denied.")
output=''
taskid=-1;
# Check required param
if not granted: return HttpResponse("access denied.")
output=''
taskid=-1;
# Check required param
- if
request.has_key('taskid')
: taskid = request['taskid']
+ if
'taskid' in request
: taskid = request['taskid']
else: return HttpResponse('missing param task id')
try:
rec = Task.objects.get(id=taskid)
mytimestamp = datetime.now().__str__()
mytimestamp = re.sub(pattern=":[^:]*$",repl="",string=mytimestamp)
else: return HttpResponse('missing param task id')
try:
rec = Task.objects.get(id=taskid)
mytimestamp = datetime.now().__str__()
mytimestamp = re.sub(pattern=":[^:]*$",repl="",string=mytimestamp)
- if
request.has_key('msg')
:
+ if
'msg' in request
:
rec.task_status += ", "+request['msg']+" ("+mytimestamp+")"
else :
rec.task_status = "Registered ("+mytimestamp+")"
rec.task_status += ", "+request['msg']+" ("+mytimestamp+")"
else :
rec.task_status = "Registered ("+mytimestamp+")"
@@
-43,13
+43,13
@@
def getProjects(request):
ClIP = request.META['REMOTE_ADDR']
#Check client access permission
granted = False
ClIP = request.META['REMOTE_ADDR']
#Check client access permission
granted = False
- if (
settings.ALLOWED_ANALYS_IPS.has_key(ClIP)
): granted = True
+ if (
ClIP in settings.ALLOWED_ANALYS_IPS
): granted = True
if not granted: return HttpResponse("access denied.")
outputfile = ''
All=False
if not granted: return HttpResponse("access denied.")
outputfile = ''
All=False
- if (
request.has_key('mode')
):
+ if (
'mode' in request
):
if request['mode']=='all':
All=True
if request['mode']=='all':
All=True
diff --git
a/htsworkflow/frontend/reports/reports.py
b/htsworkflow/frontend/reports/reports.py
index 18cd3285c5bb90b4fdeaea37292f02fdb9ade45a..e2ff54f817850babf06791e97ea26d0502af703d 100644
(file)
--- a/
htsworkflow/frontend/reports/reports.py
+++ b/
htsworkflow/frontend/reports/reports.py
@@
-27,7
+27,7
@@
def getBgColor(reads_cnt,exp_type):
def report1(request):
EXP = 'ChIP-seq'
def report1(request):
EXP = 'ChIP-seq'
- if
request.GET.has_key('aflid')
:
+ if
'aflid' in request.GET
:
AFL_Id = request.GET['aflid']
try:
AFL = Affiliation.objects.get(id=AFL_Id).name
AFL_Id = request.GET['aflid']
try:
AFL = Affiliation.objects.get(id=AFL_Id).name
@@
-170,10
+170,10
@@
def report1(request):
def report_RM(request): #for RNA-Seq and Methyl-Seq
EXP = 'RNA-seq'
def report_RM(request): #for RNA-Seq and Methyl-Seq
EXP = 'RNA-seq'
- if
request.GET.has_key('exp')
:
+ if
'exp' in request.GET
:
EXP = request.GET['exp'] # Methyl-seq
EXP = request.GET['exp'] # Methyl-seq
- if
request.GET.has_key('aflid')
:
+ if
'aflid' in request.GET
:
AFL_Id = request.GET['aflid']
try:
AFL = Affiliation.objects.get(id=AFL_Id).name
AFL_Id = request.GET['aflid']
try:
AFL = Affiliation.objects.get(id=AFL_Id).name
diff --git
a/htsworkflow/pipelines/bustard.py
b/htsworkflow/pipelines/bustard.py
index 5df79c7fb80eb3afd5cba76f536e6c194a39d533..68ecc75c1fcbc9c6c969032cdef3995c1a99a3f0 100644
(file)
--- a/
htsworkflow/pipelines/bustard.py
+++ b/
htsworkflow/pipelines/bustard.py
@@
-309,7
+309,7
@@
class Bustard(object):
# add phasing parameters
for lane in LANE_LIST:
# add phasing parameters
for lane in LANE_LIST:
- if
self.phasing.has_key(lane)
:
+ if
lane in self.phasing
:
params.append(self.phasing[lane].get_elements())
# add crosstalk matrix if it exists
params.append(self.phasing[lane].get_elements())
# add crosstalk matrix if it exists
diff --git
a/htsworkflow/pipelines/ipar.py
b/htsworkflow/pipelines/ipar.py
index 52dda0889c9b8cfc5aea23c6423e32beb2f9e1fa..8719a060cd9d1ef67a2abf0cc33e7055d4924e53 100644
(file)
--- a/
htsworkflow/pipelines/ipar.py
+++ b/
htsworkflow/pipelines/ipar.py
@@
-210,7
+210,7
@@
def load_ipar_param_tree(paramfile):
tree = ElementTree.parse(paramfile).getroot()
run = tree.find('Run')
tree = ElementTree.parse(paramfile).getroot()
run = tree.find('Run')
- if run.attrib.
has_key('Name') and run.attrib['Name']
in SOFTWARE_NAMES:
+ if run.attrib.
get('Name', None)
in SOFTWARE_NAMES:
return run
else:
LOGGER.info("No run found")
return run
else:
LOGGER.info("No run found")
diff --git
a/htsworkflow/pipelines/summary.py
b/htsworkflow/pipelines/summary.py
index 1da11a39b416f8141ca9f97c485d9477ed5dfbcb..8f454e6dbee1c8a804d7950c4c337a437dca3deb 100644
(file)
--- a/
htsworkflow/pipelines/summary.py
+++ b/
htsworkflow/pipelines/summary.py
@@
-132,7
+132,7
@@
class SummaryGA(Summary):
('Lane Results Summary : Read 1', 0),
('Lane Results Summary : Read 2', 1),]
for name, end in table_names:
('Lane Results Summary : Read 1', 0),
('Lane Results Summary : Read 2', 1),]
for name, end in table_names:
- if
tables.has_key(name)
:
+ if
name in tables
:
self._extract_lane_results_for_end(tables, name, end)
if len(self.lane_results[0]) == 0:
self._extract_lane_results_for_end(tables, name, end)
if len(self.lane_results[0]) == 0:
diff --git
a/htsworkflow/util/fctracker.py
b/htsworkflow/util/fctracker.py
index 5ba33892f741213bb1932292e5821551df379295..da90bbe68e12b9b11ce6cc10fbf7cd29755e2b6c 100644
(file)
--- a/
htsworkflow/util/fctracker.py
+++ b/
htsworkflow/util/fctracker.py
@@
-72,7
+72,7
@@
class fctracker:
lane_library = [ (x[0][5], x[1]) for x in fc.items()
if library_id_re.match(x[0]) ]
for lane, library_id in lane_library:
lane_library = [ (x[0][5], x[1]) for x in fc.items()
if library_id_re.match(x[0]) ]
for lane, library_id in lane_library:
- if
not self.library[library_id].has_key('lanes')
:
+ if
'lanes' not in self.library[library_id]
:
self.library[library_id]['lanes'] = []
self.library[library_id]['lanes'].append((fc_id, lane))
self.library[library_id]['lanes'] = []
self.library[library_id]['lanes'].append((fc_id, lane))
diff --git
a/scripts/htsw-update-archive
b/scripts/htsw-update-archive
index aeabc57ff20189d716746de5f1afa7d8494f51eb..302fbfe45abcb3e979dc0ea52fb8bde4cfd64e39 100755
(executable)
--- a/
scripts/htsw-update-archive
+++ b/
scripts/htsw-update-archive
@@
-26,7
+26,7
@@
def build_flowcell_db(fcdb_filename, sequences, baseurl, apiid, apikey):
flowcell_info = None
# get info about flowcell from server or shelf
flowcell_info = None
# get info about flowcell from server or shelf
- if
not fcdb.has_key(flowcell)
:
+ if
flowcell not in fcdb
:
url = api.flowcell_url(baseurl, flowcell)
flowcell_info = api.retrieve_info(url, apidata)
if flowcell_info is not None:
url = api.flowcell_url(baseurl, flowcell)
flowcell_info = api.retrieve_info(url, apidata)
if flowcell_info is not None: