def page(request):
if request.user.is_authenticated:
isoInfo = det.convertToJson(c.IsolateHeaderPv)
apHeader = getHeaders.getApHeaderAsJson()
ccHeader = getHeaders.getCcHeaderAsJson()
epiInfo = getHeaders.getEpiHeaderAsJson()
locInfo = det.convertToJson(c.IsoMetaLocInfoPv)
islnInfo = det.convertToJson(c.IsoMetaIslnInfoPv)
else:
isoInfo = det.convertToJson(c.IsolateHeaderPu)
apHeader = getHeaders.getApHeaderAsJson()
ccHeader = getHeaders.getCcHeaderAsJson()
epiInfo = getHeaders.getEpiHeaderAsJson()
locInfo = det.convertToJson(c.IsoMetaLocInfoPu)
islnInfo = det.convertToJson(c.IsoMetaIslnInfoPu)
return render(
request, 'Salmonella/isolateList.html', {
"isoHeader": isoInfo,
"apHeader": apHeader,
"ccHeader": ccHeader,
"epiHeader": epiInfo,
"locHeader": locInfo,
"islnHeader": islnInfo
})
def page(request):
# print("yes in this page...")
if request.user.is_authenticated:
isoInfo = det.convertToJson(c.IsolateHeaderPv)
apHeader = getHeaders.getApHeaderAsJson()
ccHeader = getHeaders.getCcHeaderAsJson()
mgtInfo = det.convertToJson(c.MgtColsPv)
epiInfo = getHeaders.getEpiHeaderAsJson()
locInfo = det.convertToJson(c.IsoMetaLocInfoPv)
islnInfo = det.convertToJson(c.IsoMetaIslnInfoPv)
else:
isoInfo = det.convertToJson(c.IsolateHeaderPu)
apHeader = getHeaders.getApHeaderAsJson()
ccHeader = getHeaders.getCcHeaderAsJson()
mgtInfo = det.convertToJson(c.MgtColsPu)
epiInfo = getHeaders.getEpiHeaderAsJson()
locInfo = det.convertToJson(c.IsoMetaLocInfoPu)
islnInfo = det.convertToJson(c.IsoMetaIslnInfoPu)
isAp = True
isDst = False
isMgtColor = True
if 'isAp' in request.POST and request.POST['isAp'] == "false":
isAp = False
if 'isDst' in request.POST and request.POST['isDst'] == 'true':
isDst = True
if 'isMgtColor' in request.POST and request.POST['isMgtColor'] == 'false':
isMgtColor = False
sessionVar = list()
pageNumToGet = 1
orderBy = None
dir = None
isCsv = False
maxIsolatesPerPage = c.TOTAL_ISO_PER_PAGE
searchAp = []
searchCcEpi = []
searchLocs = []
searchIsln = []
searchProj = []
if (('orderBy' in request.POST and len(request.POST['orderBy']) > 0) or
('pageNumToGet' in request.POST and len(request.POST['pageNumToGet']) >
0)) or ('isCsv' in request.POST and request.POST['isCsv'] == 'true'):
sessionVar_json = request.session['sessionVar']
sessionVar = json.loads(sessionVar_json)
if sessionVar[0]['pageType'] != cl.SearchIsolateDetail:
raise Http404()
(searchAp, searchCcEpi, searchLocs, searchIsln,
searchProj) = ses.loadSessionSearchVars_detail(sessionVar)
if 'orderBy' in request.POST and len(request.POST['orderBy']) > 0:
orderBy = request.POST['orderBy']
dir = request.POST['dir']
# update session with posted values
sessionVar[0]['orderBy'] = orderBy
sessionVar[0]['dir'] = dir
pageNumToGet = ses.loadIfInSession(sessionVar, 'pageNumToGet', 1)
if 'pageNumToGet' in request.POST and len(
request.POST['pageNumToGet']) > 0:
pageNumToGet = int(request.POST['pageNumToGet'])
# update session with posted values
sessionVar[0]['pageNumToGet'] = pageNumToGet
orderBy = ses.loadIfInSession(sessionVar, 'orderBy', None)
dir = ses.loadIfInSession(sessionVar, 'dir', None)
if ('isCsv' in request.POST and request.POST['isCsv'] == 'true'):
isCsv = True
maxIsolatesPerPage = c.TOTAL_ISO_PER_DOWNLOAD
elif ses.isASearchPresent_detail(request.POST):
# a new search has been initiated
sessionVar.append(dict())
(searchAp, searchCcEpi, searchLocs, searchIsln,
searchProj) = loadRequestSearchVars_detail(request.POST)
sessionVar[0]['json_apSearchTerms'] = searchAp
sessionVar[0]['json_ccEpiSearchTerms'] = searchCcEpi
sessionVar[0]['json_location'] = searchLocs
sessionVar[0]['json_isolation'] = searchIsln
sessionVar[0]['json_project'] = searchProj
sessionVar[0]['pageType'] = cl.SearchIsolateDetail
else:
raise Http404('Search variables not found!')
json_sessionVar = json.dumps(sessionVar, cls=DjangoJSONEncoder)
request.session['sessionVar'] = json_sessionVar
# print("updated version")
# print (searchVar)
###########################
arr_ap = []
arr_ccEpi = []
arr_iso = []
arr_isln = []
arr_loc = []
if searchAp:
arr_ap = [searchAp]
if searchCcEpi:
arr_ccEpi = [searchCcEpi]
if searchLocs:
arr_loc = [searchLocs]
if searchIsln:
arr_isln = [searchIsln]
if searchProj:
projectId = Project.objects.get(identifier=searchProj['project']).id
if not routeToRightFnAuth.isProjectByUser(projectId,
request.user.username):
raise Http404("Error you dont have access to page. Go back.")
searchProj['project'] = projectId
arr_iso = [searchProj]
if request.user.is_authenticated:
(isoCount, isolates, dict_pageInfo,
dict_mergedIds) = routeToRightFnAuth.getIsolatesFromRightFn(
arr_ap, arr_ccEpi, [], arr_loc, arr_isln, arr_iso, pageNumToGet,
maxIsolatesPerPage, request.user.username, True, orderBy, dir)
else:
(isoCount, isolates, dict_pageInfo,
dict_mergedIds) = routeToRightFnAuth.getIsolatesFromRightFn(
[searchAp], [searchCcEpi], [], [searchLocs], [searchIsln], [],
pageNumToGet, maxIsolatesPerPage, None, None, orderBy, dir)
mergedIds = det.convertToJson_dict(dict_mergedIds)
if isCsv:
outstring = makeCsv(isolates, request.user.is_authenticated)
return HttpResponse(outstring)
else:
jsonIso = det.convertToJson(isolates)
outdata = {
"isolates": jsonIso,
"isoCount": isoCount,
"pageInfo": dict_pageInfo,
"isAp": isAp,
'isDst': isDst,
'isMgtColor': isMgtColor,
"colIsoId": c.IsolateId,
"isoInfo": isoInfo,
"apInfo": apHeader,
"ccInfo": ccHeader,
"mgtInfo": mgtInfo,
"epiInfo": epiInfo,
"locInfo": locInfo,
"islnInfo": islnInfo,
"mergedIds": mergedIds
}
return render(request, 'Salmonella/isolateTable.html', outdata)
def page(request):
sessionVar = list()
pageNumToGet = 1
orderBy = None
dir = None
isCsv = False
maxIsolatesPerPage = c.TOTAL_ISO_PER_PAGE
arr_ap = []
arr_cc = []
arr_epi = []
arr_iso = []
arr_isln = []
arr_loc = []
if (('orderBy' in request.POST and len(request.POST['orderBy']) > 0) or
('pageNumToGet' in request.POST and len(request.POST['pageNumToGet']) >
0)) or ('isCsv' in request.POST and request.POST['isCsv'] == 'true'):
# session var should be reused and updated
sessionVar_json = request.session['sessionVar']
sessionVar = json.loads(sessionVar_json)
if sessionVar[0]['pageType'] != cl.SearchIsolateList:
raise Http404()
(arr_ap, arr_cc, arr_epi, arr_iso, arr_isln,
arr_loc) = ses.loadSessionSearchVars(sessionVar)
if 'orderBy' in request.POST and len(request.POST['orderBy']) > 0:
orderBy = request.POST['orderBy']
dir = request.POST['dir']
# update session with posted values
sessionVar[0]['orderBy'] = orderBy
sessionVar[0]['dir'] = dir
pageNumToGet = ses.loadIfInSession(sessionVar, 'pageNumToGet', 1)
if 'pageNumToGet' in request.POST and len(
request.POST['pageNumToGet']) > 0:
pageNumToGet = int(request.POST['pageNumToGet'])
# update session with posted values
sessionVar[0]['pageNumToGet'] = pageNumToGet
orderBy = ses.loadIfInSession(sessionVar, 'orderBy', None)
dir = ses.loadIfInSession(sessionVar, 'dir', None)
if ('isCsv' in request.POST and request.POST['isCsv'] == 'true'):
isCsv = True
maxIsolatesPerPage = c.TOTAL_ISO_PER_DOWNLOAD
elif ses.isASearchPresent(request.POST):
sessionVar.append(dict())
(arr_ap, arr_cc, arr_epi, arr_iso, arr_isln,
arr_loc) = ses.loadRequestSearchVars(request.POST)
sessionVar[0]['arrAp'] = arr_ap
sessionVar[0]['arrCc'] = arr_cc
sessionVar[0]['arrEpi'] = arr_epi
sessionVar[0]['arrIso'] = arr_iso
sessionVar[0]['arrIsln'] = arr_isln
sessionVar[0]['arrLoc'] = arr_loc
sessionVar[0]['pageType'] = cl.SearchIsolateList
else:
raise Http404('No search variables found')
json_sessionVar = json.dumps(sessionVar, cls=DjangoJSONEncoder)
request.session['sessionVar'] = json_sessionVar
########################
isAp = True
isDst = False
isMgtColor = True
if 'isAp' in request.POST and request.POST['isAp'] == "false":
isAp = False
if 'isDst' in request.POST and request.POST['isDst'] == 'true':
isDst = True
if 'isMgtColor' in request.POST and request.POST['isMgtColor'] == 'false':
isMgtColor = False
# HEADERS
if request.user.is_authenticated:
isoInfo = det.convertToJson(c.IsolateHeaderPv)
apHeader = getHeaders.getApHeaderAsJson()
ccHeader = getHeaders.getCcHeaderAsJson()
mgtInfo = det.convertToJson(c.MgtColsPv)
epiInfo = getHeaders.getEpiHeaderAsJson()
locInfo = det.convertToJson(c.IsoMetaLocInfoPv)
islnInfo = det.convertToJson(c.IsoMetaIslnInfoPv)
(isoCount, isolates, dict_pageInfo,
dict_mergedIds) = routeToRightFnAuth.getIsolatesFromRightFn(
arr_ap, arr_cc, arr_epi, arr_loc, arr_isln, arr_iso, pageNumToGet,
maxIsolatesPerPage, request.user.username, False, orderBy, dir)
else:
isoInfo = det.convertToJson(c.IsolateHeaderPu)
apHeader = getHeaders.getApHeaderAsJson()
ccHeader = getHeaders.getCcHeaderAsJson()
mgtInfo = det.convertToJson(c.MgtColsPu)
epiInfo = getHeaders.getEpiHeaderAsJson()
locInfo = det.convertToJson(c.IsoMetaLocInfoPu)
islnInfo = det.convertToJson(c.IsoMetaIslnInfoPu)
# print("is not authenticated")
(isoCount, isolates, dict_pageInfo,
dict_mergedIds) = routeToRightFnAuth.getIsolatesFromRightFn(
arr_ap, arr_cc, arr_epi, arr_loc, arr_isln, arr_iso, pageNumToGet,
maxIsolatesPerPage, None, False, orderBy, dir)
mergedIds = det.convertToJson_dict(dict_mergedIds)
# print(dict_mergedIds)
if isCsv:
outstring = makeCsv(isolates, request.user.is_authenticated)
return HttpResponse(outstring)
else:
jsonIso = det.convertToJson(isolates)
return render(
request, 'Salmonella/isolateTable.html', {
"isolates": jsonIso,
"isoCount": isoCount,
"pageInfo": dict_pageInfo,
"isAp": isAp,
'isDst': isDst,
'isMgtColor': isMgtColor,
"colIsoId": c.IsolateId,
"isoInfo": isoInfo,
"apInfo": apHeader,
"ccInfo": ccHeader,
"mgtInfo": mgtInfo,
"epiInfo": epiInfo,
"locInfo": locInfo,
"islnInfo": islnInfo,
"mergedIds": mergedIds
})
def page(request):
sessionVar = list()
pageNumToGet = 1
orderBy = None
dir = None
isCsv = False
maxIsolatesPerPage = c.TOTAL_ISO_PER_PAGE
if (('orderBy' in request.POST and len(request.POST['orderBy']) > 0) or
('pageNumToGet' in request.POST and len(request.POST['pageNumToGet']) >
0)) or ('isCsv' in request.POST and request.POST['isCsv'] == 'true'):
# session var should be reused and updated
sessionVar_json = request.session['sessionVar']
sessionVar = json.loads(sessionVar_json)
if sessionVar[0]['pageType'] != cl.InitialIsolates:
raise Http404()
if 'orderBy' in request.POST and len(request.POST['orderBy']) > 0:
orderBy = request.POST['orderBy']
dir = request.POST['dir']
print(orderBy + " . ... . " + dir)
# update session with posted values
sessionVar[0]['orderBy'] = orderBy
sessionVar[0]['dir'] = dir
pageNumToGet = ses.loadIfInSession(sessionVar, 'pageNumToGet', 1)
if 'pageNumToGet' in request.POST and len(
request.POST['pageNumToGet']) > 0:
pageNumToGet = int(request.POST['pageNumToGet'])
# update session with posted values
sessionVar[0]['pageNumToGet'] = pageNumToGet
orderBy = ses.loadIfInSession(sessionVar, 'orderBy', None)
dir = ses.loadIfInSession(sessionVar, 'dir', None)
if ('isCsv' in request.POST and request.POST['isCsv'] == 'true'):
isCsv = True
maxIsolatesPerPage = c.TOTAL_ISO_PER_DOWNLOAD
else:
# load all public data
sessionVar.append(dict())
sessionVar[0]['pageType'] = cl.InitialIsolates
json_sessionVar = json.dumps(sessionVar, cls=DjangoJSONEncoder)
request.session['sessionVar'] = json_sessionVar
############################
isoCount = 0
dict_pageInfo = dict()
isolates = []
if request.user.is_authenticated:
isoInfo = det.convertToJson(c.IsolateHeaderPv)
apHeader = getHeaders.getApHeaderAsJson()
ccHeader = getHeaders.getCcHeaderAsJson()
mgtInfo = det.convertToJson(c.MgtColsPv)
epiInfo = getHeaders.getEpiHeaderAsJson()
locInfo = det.convertToJson(c.IsoMetaLocInfoPv)
islnInfo = det.convertToJson(c.IsoMetaIslnInfoPv)
(isoCount, isolates, dict_pageInfo,
dict_mergedIds) = routeToRightFnAuth.getIsolatesFromRightFn(
[], [], [], [], [], [], pageNumToGet, maxIsolatesPerPage,
request.user.username, None, orderBy, dir)
else:
isoInfo = det.convertToJson(c.IsolateHeaderPu)
apHeader = getHeaders.getApHeaderAsJson()
ccHeader = getHeaders.getCcHeaderAsJson()
mgtInfo = det.convertToJson(c.MgtColsPu)
epiInfo = getHeaders.getEpiHeaderAsJson()
locInfo = det.convertToJson(c.IsoMetaLocInfoPu)
islnInfo = det.convertToJson(c.IsoMetaIslnInfoPu)
(isoCount, isolates, dict_pageInfo,
dict_mergedIds) = routeToRightFnAuth.getIsolatesFromRightFn(
[], [], [], [], [], [], pageNumToGet, maxIsolatesPerPage, None,
None, orderBy, dir)
isAp = True
isDst = False
isMgtColor = True
if 'isAp' in request.POST and request.POST['isAp'] == "false":
isAp = False
if 'isDst' in request.POST and request.POST['isDst'] == 'true':
isDst = True
if 'isMgtColor' in request.POST and request.POST['isMgtColor'] == 'false':
isMgtColor = False
# print ("is mgtcolor is " + str(isMgtColor) + " ... " + request.POST['isAp'])
# print(' GETTING TO THE END!')
if isCsv:
outstring = makeCsv(isolates, request.user.is_authenticated)
return HttpResponse(outstring)
else:
isolatesjson = det.convertToJson(isolates)
return render(
request, 'Salmonella/isolateTable.html', {
"isolates": isolatesjson,
"isoCount": isoCount,
"pageInfo": dict_pageInfo,
"isAp": isAp,
"colIsoId": c.IsolateId,
"isoInfo": isoInfo,
"apInfo": apHeader,
"ccInfo": ccHeader,
"mgtInfo": mgtInfo,
"epiInfo": epiInfo,
"locInfo": locInfo,
"islnInfo": islnInfo,
"isDst": isDst,
"isMgtColor": isMgtColor
})
def page(request):
if not request.user.is_authenticated:
raise Http404("You need to log in to view this page!")
else:
isoInfo = det.convertToJson(c.IsolateHeaderPv)
apHeader = getHeaders.getApHeaderAsJson()
ccHeader = getHeaders.getCcHeaderAsJson()
mgtInfo = det.convertToJson(c.MgtColsPv)
epiInfo = getHeaders.getEpiHeaderAsJson()
locInfo = det.convertToJson(c.IsoMetaLocInfoPv)
islnInfo = det.convertToJson(c.IsoMetaIslnInfoPv)
sessionVar = list()
pageNumToGet = 1
orderBy = None
dir = None
isCsv = False;
maxIsolatesPerPage = c.TOTAL_ISO_PER_PAGE
arr_ap = []; arr_cc = []; arr_epi = []; arr_iso = []; arr_isln = []; arr_loc = [];
if (('orderBy' in request.POST and len(request.POST['orderBy']) > 0) or ('pageNumToGet' in request.POST and len(request.POST['pageNumToGet']) > 0)) or ('isCsv' in request.POST and request.POST['isCsv'] == 'true'):
# get variables from session
sessionVar_json = request.session['sessionVar']
sessionVar = json.loads(sessionVar_json)
if sessionVar[0]['pageType'] != cl.SearchProjectDetail:
raise Http404()
(arr_ap, arr_cc, arr_epi, arr_iso, arr_isln, arr_loc) = ses.loadSessionSearchVars(sessionVar)
projectId = sessionVar[0]['projectId']
if 'orderBy' in request.POST and len(request.POST['orderBy']) > 0:
orderBy = request.POST['orderBy']
dir = request.POST['dir']
# update session with posted values
sessionVar[0]['orderBy'] = orderBy
sessionVar[0]['dir'] = dir
pageNumToGet = ses.loadIfInSession(sessionVar, 'pageNumToGet', 1)
if 'pageNumToGet' in request.POST and len(request.POST['pageNumToGet']) > 0:
pageNumToGet = int(request.POST['pageNumToGet'])
# update session with posted values
sessionVar[0]['pageNumToGet'] = pageNumToGet
orderBy = ses.loadIfInSession(sessionVar, 'orderBy', None)
dir = ses.loadIfInSession(sessionVar, 'dir', None)
if ('isCsv' in request.POST and request.POST['isCsv'] == 'true'):
isCsv = True;
maxIsolatesPerPage = c.TOTAL_ISO_PER_DOWNLOAD
elif 'projectId' in request.POST and len(request.POST['projectId']) > 0 and ses.isASearchPresent(request.POST):
# a new search has been initiated
sessionVar.append(dict())
(arr_ap, arr_cc, arr_epi, arr_iso, arr_isln, arr_loc, projectId) = loadRequestSearchVars_proj(request.POST) # adds project id to arr_iso
sessionVar[0]['arrAp'] = arr_ap
sessionVar[0]['arrCc'] = arr_cc
sessionVar[0]['arrEpi'] = arr_epi
sessionVar[0]['arrIso'] = arr_iso
sessionVar[0]['arrIsln'] = arr_isln
sessionVar[0]['arrLoc'] = arr_loc
sessionVar[0]['projectId'] = projectId
sessionVar[0]['pageType'] = cl.SearchProjectDetail
else:
raise Http404("Desired vars not in search")
# CHECK! if use has the right access rights
if not Project.objects.filter(id=int(projectId),user=User.objects.get(userId=request.user)).exists():
return Http404("Error: you dont have permission to access this page!")
json_sessionVar = json.dumps(sessionVar, cls=DjangoJSONEncoder)
request.session['sessionVar'] = json_sessionVar
#########################
isAp = True; isDst = False; isMgtColor = True;
if 'isAp' in request.POST and request.POST['isAp'] == "false":
isAp = False
if 'isDst' in request.POST and request.POST['isDst'] == 'true':
isDst = True
if 'isMgtColor' in request.POST and request.POST['isMgtColor'] == 'false':
isMgtColor = False
(isoCount, isolates, dict_pageInfo, dict_mergedIds) = routeToRightFnAuth.getIsolatesFromRightFn(arr_ap, arr_cc, arr_epi, arr_loc, arr_isln, arr_iso, pageNumToGet, maxIsolatesPerPage, request.user.username, True, orderBy, dir)
mergedIds = det.convertToJson_dict(dict_mergedIds)
if isCsv:
outstring = makeCsv(isolates,request.user.is_authenticated)
return HttpResponse(outstring)
else:
jsonIso = det.convertToJson(isolates)
return render(request, 'Salmonella/isolateTable.html', {"isolates": jsonIso, "IsolateId": c.IsolateId, "isAp": isAp, 'isDst': isDst, 'isMgtColor': isMgtColor, "colIsoId": c.IsolateId, "isoInfo": isoInfo, "apInfo": apHeader, "ccInfo": ccHeader, "mgtInfo": mgtInfo, "epiInfo": epiInfo, "locInfo": locInfo, "islnInfo": islnInfo, "isoCount": isoCount, "pageInfo": dict_pageInfo, "mergedIds": mergedIds})
def page(request, pk):
userProjIds = list()
if request.user.is_authenticated:
isoInfo = det.convertToJson(c.IsolateHeaderPv)
apHeader = getHeaders.getApHeaderAsJson()
ccHeader = getHeaders.getCcHeaderAsJson()
epiInfo = getHeaders.getEpiHeaderAsJson()
locInfo = det.convertToJson(c.IsoMetaLocInfoPv)
islnInfo = det.convertToJson(c.IsoMetaIslnInfoPv)
projHeader = det.convertToJson(c.ProjHeaderPv)
userProjIds = q.getUserProjectIds(request.user.username)
else:
isoInfo = det.convertToJson(c.IsolateHeaderPu)
apHeader = getHeaders.getApHeaderAsJson()
ccHeader = getHeaders.getCcHeaderAsJson()
epiInfo = getHeaders.getEpiHeaderAsJson()
locInfo = det.convertToJson(c.IsoMetaLocInfoPu)
islnInfo = det.convertToJson(c.IsoMetaIslnInfoPu)
projHeader = []
# check pk refers to public strain, then return.
isolate = None
isoMgt = None
json_isoMgt = {}
isUserIso = False
try:
isolate = Isolate.objects.get(pk=pk)
except Isolate.DoesNotExist:
raise Http404("Isolate does not exist")
if isolate.server_status == 'C' and isolate.assignment_status == 'A':
print(str(isolate) + " !!")
isoMgt = View_apcc.objects.get(mgt_id=isolate.mgt)
if isoMgt:
json_isoMgt = serializers.serialize('json', [isoMgt])
if len(userProjIds) > 0:
if isolate.project_id in userProjIds:
isUserIso = True
project = Project.objects.get(pk=isolate.project_id)
return render(
request, 'Salmonella/isolateDetail.html', {
"isoHeader": isoInfo,
"apHeader": apHeader,
"ccHeader": ccHeader,
"epiHeader": epiInfo,
"locHeader": locInfo,
"islnHeader": islnInfo,
"isolate": isolate,
"json_isoHgt": json_isoMgt,
"projHeader": projHeader,
"isUserIso": isUserIso
}
) # {"isolate": isolate, "json_isoHgt": json_isoMgt }) # }) # "similar_strains": qs_similarAps},)