def updateTag(request):
# read in the crucial parameters
tagKey = request.PUT.get('id', None)
if not tagKey:
raise Errors.MISSING_PARAMETER.setCustom('id')
points = request.PUT.get('points', None)
if points:
try:
points = json.loads(points)
except ValueError:
raise Errors.INVALID_SYNTAX.setCustom('points')
else:
raise Errors.MISSING_PARAMETER.setCustom('points')
color = request.PUT.get('color', None)
if color:
try:
color = json.loads(color)
except ValueError:
color = Util.getDelimitedList(request.PUT, 'color')
else:
raise Errors.MISSING_PARAMETER.setCustom('color')
name = request.PUT.get('name', None)
if not name:
raise Errors.MISSING_PARAMETER.setCustom('name')
# read in optional parameters and initialize the API
fields = Util.getDelimitedList(request.PUT, 'fields')
putAPI = PutAPI(request.user, fields)
return putAPI.updateTag(tagKey, points, name, color)
def updateTag(request):
# read in the crucial parameters
tagKey = request.PUT.get('id', None)
if not tagKey:
raise Errors.MISSING_PARAMETER.setCustom('id')
points = request.PUT.get('points', None)
if points:
try:
points = json.loads(points)
except ValueError:
raise Errors.INVALID_SYNTAX.setCustom('points')
else:
raise Errors.MISSING_PARAMETER.setCustom('points')
color = request.PUT.get('color', None)
if color:
try:
color = json.loads(color)
except ValueError:
color = Util.getDelimitedList(request.PUT, 'color')
else:
raise Errors.MISSING_PARAMETER.setCustom('color')
name = request.PUT.get('name', None)
if not name:
raise Errors.MISSING_PARAMETER.setCustom('name')
# read in optional parameters and initialize the API
fields = Util.getDelimitedList(request.PUT, 'fields')
putAPI = PutAPI(request.user, fields)
return putAPI.updateTag(tagKey, points, name, color)
def doProcessRender(self, request):
self.addPageletBinding('navBar', NavBarPagelet())
numSearch = 0
searchImageDesc = str(request.GET.get('searchImageDesc',
'')).lower() == "true"
searchImageNotes = str(request.GET.get('searchImageNotes',
'')).lower() == "true"
searchGeneName = str(request.GET.get('searchGeneName',
'')).lower() == "true"
searchGeneSymbol = str(request.GET.get('searchGeneSymbol',
'')).lower() == "true"
searchGeneID = str(request.GET.get('searchGeneID',
'')).lower() == "true"
query = Util.getDelimitedList(request.GET, 'query')
#print searchImageDesc
#print searchImageNotes
#print searchGeneName
#print searchGeneSymbol
#print searchGeneID
candidate_cat = []
if searchImageDesc:
query = Util.getDelimitedList(request.GET, 'query')
print query
print len(query)
candidates_ImgDesc = []
candidate_cat.append('Image Description')
if query:
pictures = Picture.objects.filter(
description__icontains=query[0])
print pictures
candidates_ImgDesc.append(pictures)
formatQuery = ""
if query:
formatQuery += 'General Query: "' + ", ".join(query) + '"'
search = {
'candidate_cat': candidate_cat,
'candidates_ImgDesc': candidates_ImgDesc,
'query': formatQuery
}
#if searchImageDesc:
numSearch += 1
self.addPageletBinding('center-' + str(numSearch),
ImageSearchPagelet().setSearchParams(search))
args = {'title': 'Search', 'numPagelets': numSearch}
self.setApplicationLayout('public/search.html', args)
self.addPageletBinding('footer', FooterPagelet())
def getOrganisms(request):
# get the list of organisms (base on comma delimited list)
organisms = Util.getDelimitedList(request.GET, 'organisms')
# optional parameters
fields = Util.getDelimitedList(request.GET, 'fields')
getAPI = GetAPI(request.user, fields)
return getAPI.getOrganisms(organisms)
def getOrganisms(request):
# get the list of organisms (base on comma delimited list)
organisms = Util.getDelimitedList(request.GET, 'organisms')
# optional parameters
fields = Util.getDelimitedList(request.GET, 'fields')
getAPI = GetAPI(request.user, fields)
return getAPI.getOrganisms(organisms)
def getImageTags(request):
renderObj = WebServiceObject()
# read in crucial parameters
tagGroupKey = request.GET.get('tagGroupId', None)
imageKey = request.GET.get('imageId', None)
# read in optional parameters and initialize the API
offset = Util.getInt(request.GET, 'offset', 0)
limit = Util.getInt(request.GET, 'limit', 10)
unlimited = request.GET.get('unlimited', False)
fields = Util.getDelimitedList(request.GET, 'fields')
getAPI = GetAPI(limit, offset, request.user, fields, unlimited)
if tagGroupKey:
# the key for lookup and the image it is attached to
renderObj = getAPI.getTagsByTagGroup(tagGroupKey, isKey=True)
elif imageKey:
# the key for lookup and the image it is attached to
renderObj = getAPI.getTagsByImage(imageKey, isKey=True)
else:
# get all the tags
renderObj = getAPI.getTags()
return renderObj
def getImageTags(request):
renderObj = WebServiceObject()
# read in crucial parameters
tagGroupKey = request.GET.get('tagGroupId', None)
imageKey = request.GET.get('imageId', None)
# read in optional parameters and initialize the API
offset = Util.getInt(request.GET, 'offset', 0)
limit = Util.getInt(request.GET, 'limit', 10)
unlimited = request.GET.get('unlimited', False)
fields = Util.getDelimitedList(request.GET, 'fields')
getAPI = GetAPI(limit, offset, request.user, fields, unlimited)
if tagGroupKey:
# the key for lookup and the image it is attached to
renderObj = getAPI.getTagsByTagGroup(tagGroupKey, isKey=True)
elif imageKey:
# the key for lookup and the image it is attached to
renderObj = getAPI.getTagsByImage(imageKey, isKey=True)
else:
# get all the tags
renderObj = getAPI.getTags()
return renderObj
def getQtl(request):
imageKey = request.GET.get('pictureID', None)
# read in optional parameters and initialize the API
fields = Util.getDelimitedList(request.GET, 'fields')
getAPI = GetAPI(request.user, fields)
return getAPI.getQtl(imageKey)
def createImageMetadata(request):
renderObj = WebServiceObject()
# these should overwrite current metadata
image = request.FILES.get('image', None)
description = request.POST.get('description', None)
altText = request.POST.get('altText', None)
organisms = Util.getDelimitedList(request.POST, 'organisms')
fields = Util.getDelimitedList(request.POST, 'fields')
if image:
postAPI = PostAPI(request.user, fields)
renderObj = postAPI.createImageMetadata(image, description, altText, organisms)
else:
raise Errors.MISSING_PARAMETER.setCustom('image')
return renderObj
def getImageMetadata(request):
#optional parameters
offset = Util.getInt(request.GET, 'offset', 0)
limit = Util.getInt(request.GET, 'limit', 10)
unlimited = request.GET.get('unlimited', False)
fields = Util.getDelimitedList(request.GET, 'fields')
getAPI = GetAPI(limit, offset, request.user, fields, unlimited)
if request.GET.has_key('by'):
by = request.GET['by']
if by == 'organism':
# required paramaters
organismIds = Util.getDelimitedList(request.GET, 'organismId')
return getAPI.getImageMetadataByOrganism(organismIds)
else:
raise Errors.INVALID_PARAMETER.setCustom('by')
else:
return getAPI.getImageMetadata()
def createImageMetadata(request):
renderObj = WebServiceObject()
# these should overwrite current metadata
image = request.FILES.get('image', None)
description = request.POST.get('description', None)
altText = request.POST.get('altText', None)
organisms = Util.getDelimitedList(request.POST, 'organisms')
fields = Util.getDelimitedList(request.POST, 'fields')
if image:
postAPI = PostAPI(request.user, fields)
renderObj = postAPI.createImageMetadata(image, description, altText,
organisms)
else:
raise Errors.MISSING_PARAMETER.setCustom('image')
return renderObj
def deleteImage(request):
# required parameters
imageKey = request.DELETE.get('id', None)
if not imageKey:
raise Errors.NO_IMAGE_KEY
fields = Util.getDelimitedList(request.GET, 'fields')
deleteAPI = DeleteAPI(request.user, fields)
return deleteAPI.deleteImage(imageKey)
def deleteImage(request):
# required parameters
imageKey = request.DELETE.get('id', None)
if not imageKey:
raise Errors.NO_IMAGE_KEY
fields = Util.getDelimitedList(request.GET, 'fields')
deleteAPI = DeleteAPI(request.user, fields)
return deleteAPI.deleteImage(imageKey)
def deleteTagGroup(request):
tagGroupKey = request.DELETE.get("id", None)
if not tagGroupKey:
raise Errors.MISSING_PARAMETER.setCustom("id")
# get optional parameter
fields = Util.getDelimitedList(request.DELETE, "fields")
deleteAPI = DeleteAPI(request.user, fields)
return deleteAPI.deleteTagGroup(tagGroupKey)
def deleteTagGroup(request):
tagGroupKey = request.DELETE.get('id', None)
if not tagGroupKey:
raise Errors.MISSING_PARAMETER.setCustom('id')
# get optional parameter
fields = Util.getDelimitedList(request.DELETE, 'fields')
deleteAPI = DeleteAPI(request.user, fields)
return deleteAPI.deleteTagGroup(tagGroupKey)
def editImageMetadata(request):
renderObj = WebServiceObject()
# required parameters
imageKey = request.PUT.get('id', None)
if not imageKey:
raise Errors.NO_IMAGE_KEY
# these should overwrite current metadata
description = request.PUT.get('description', None)
altText = request.POST.get('altText', None)
organisms = Util.getDelimitedList(request.PUT, 'organisms')
fields = Util.getDelimitedList(request.PUT, 'fields')
if description or organisms:
putAPI = PutAPI(request.user, fields)
renderObj = putAPI.editImageMetadata(imageKey, description, altText, organisms)
else:
raise Errors.NOT_MODIFIED
return renderObj
def editImageMetadata(request):
renderObj = WebServiceObject()
# required parameters
imageKey = request.PUT.get('id', None)
if not imageKey:
raise Errors.NO_IMAGE_KEY
# these should overwrite current metadata
description = request.PUT.get('description', None)
altText = request.POST.get('altText', None)
organisms = Util.getDelimitedList(request.PUT, 'organisms')
fields = Util.getDelimitedList(request.PUT, 'fields')
if description or organisms:
putAPI = PutAPI(request.user, fields)
renderObj = putAPI.editImageMetadata(imageKey, description, altText,
organisms)
else:
raise Errors.NOT_MODIFIED
return renderObj
def getGeneLink(request):
# read in crucial parameters
geneLinkKey = request.GET.get('id', None)
# read in optional parameters and initialize the API
fields = Util.getDelimitedList(request.GET, 'fields')
getAPI = GetAPI(request.user, fields)
if not geneLinkKey:
raise Errors.NO_GENE_LINK_KEY
# the key for lookup and the image it is attached to
return getAPI.getGeneLink(geneLinkKey)
def getTagGroup(request):
# read in crucial parameters
tagGroupKey = request.GET.get("id", None)
# read in optional parameters and initialize the API
fields = Util.getDelimitedList(request.GET, "fields")
getAPI = GetAPI(request.user, fields)
if not tagGroupKey:
raise Errors.NO_TAG_GROUP_KEY
# the key for lookup and the image it is attached to
return getAPI.getTagGroup(tagGroupKey)
def getGeneLink(request):
# read in crucial parameters
geneLinkKey = request.GET.get('id', None)
# read in optional parameters and initialize the API
fields = Util.getDelimitedList(request.GET, 'fields')
getAPI = GetAPI(request.user, fields)
if not geneLinkKey:
raise Errors.NO_GENE_LINK_KEY
# the key for lookup and the image it is attached to
return getAPI.getGeneLink(geneLinkKey)
def getTagGroup(request):
# read in crucial parameters
tagGroupKey = request.GET.get('id', None)
# read in optional parameters and initialize the API
fields = Util.getDelimitedList(request.GET, 'fields')
getAPI = GetAPI(request.user, fields)
if not tagGroupKey:
raise Errors.NO_TAG_GROUP_KEY
# the key for lookup and the image it is attached to
return getAPI.getTagGroup(tagGroupKey)
def deleteTag(request):
geneLinkKey = request.DELETE.get('id', None)
if not geneLinkKey:
raise Errors.MISSING_PARAMETER.setCustom('id')
# get optional parameter
fields = Util.getDelimitedList(request.DELETE, 'fields')
deleteAPI = DeleteAPI(request.user, fields)
return deleteAPI.deleteGeneLink(geneLinkKey)
def addNote(request):
# get new note information
notes = request.POST.get('notes', None)
pn_id = request.POST.get('pn_id', None)
imageKey = request.POST.get('pictureID', None)
if not imageKey:
raise Errors.NO_IMAGE_KEY
# read in optional parameters and initialize the API
fields = Util.getDelimitedList(request.POST, 'fields')
postAPI = PostAPI(request.user, fields)
return postAPI.addNote(notes, pn_id, imageKey)
def getImageTagGroups(request):
# the key for lookup and the image it is attached to
imageKey = request.GET.get('imageId', None)
offset = Util.getInt(request.GET, 'offset', 0)
limit = Util.getInt(request.GET, 'limit', 10)
unlimited = request.GET.get('unlimited', False)
fields = Util.getDelimitedList(request.GET, 'fields')
getAPI = GetAPI(limit, offset, request.user, fields, unlimited)
if imageKey:
return getAPI.getTagGroupsByImage(imageKey)
else:
return getAPI.getTagGroups()
def createTag(request):
# get the tagGroupKey
tagGroupKey = request.POST.get('tagGroupId', None)
if not tagGroupKey:
raise Errors.NO_TAG_GROUP_KEY
# get the points
points = request.POST.get('points', None)
if points:
try:
points = json.loads(points)
except ValueError:
raise Errors.INVALID_SYNTAX.setCustom('points')
else:
raise Errors.MISSING_PARAMETER.setCustom('points')
# get the color
color = request.POST.get('color', None)
if color:
try:
color = json.loads(color)
except ValueError:
color = Util.getDelimitedList(request.PUT, 'color')
else:
raise Errors.MISSING_PARAMETER.setCustom('color')
# get the description
name = request.POST.get('name', None)
if not name:
raise Errors.MISSING_PARAMETER.setCustom('name')
# read in optional parameters and initialize the API
fields = Util.getDelimitedList(request.POST, 'fields')
postAPI = PostAPI(request.user, fields)
return postAPI.createTag(tagGroupKey, points, name, color)
def getImageMetadata(request):
renderObj = WebServiceObject()
if request.GET.has_key('id'):
# the key for lookup and the image it is attached to
imageKey = request.GET['id']
fields = Util.getDelimitedList(request.GET, 'fields')
getAPI = GetAPI(request.user, fields)
try:
renderObj = getAPI.getImageMetadata(imageKey)
except Errors.WebServiceException as e:
renderObj.setError(e)
else:
renderObj.setError(Errors.NO_IMAGE_KEY)
return renderObj
def createTag(request):
# get the tagGroupKey
tagGroupKey = request.POST.get('tagGroupId', None)
if not tagGroupKey:
raise Errors.NO_TAG_GROUP_KEY
# get the points
points = request.POST.get('points', None)
if points:
try:
points = json.loads(points)
except ValueError:
raise Errors.INVALID_SYNTAX.setCustom('points')
else:
raise Errors.MISSING_PARAMETER.setCustom('points')
# get the color
color = request.POST.get('color', None)
if color:
try:
color = json.loads(color)
except ValueError:
color = Util.getDelimitedList(request.PUT, 'color')
else:
raise Errors.MISSING_PARAMETER.setCustom('color')
# get the description
name = request.POST.get('name', None)
if not name:
raise Errors.MISSING_PARAMETER.setCustom('name')
# read in optional parameters and initialize the API
fields = Util.getDelimitedList(request.POST, 'fields')
postAPI = PostAPI(request.user, fields)
return postAPI.createTag(tagGroupKey, points, name, color)
def getImageMetadata(request):
renderObj = WebServiceObject()
if request.GET.has_key('id'):
# the key for lookup and the image it is attached to
imageKey = request.GET['id']
fields = Util.getDelimitedList(request.GET, 'fields')
getAPI = GetAPI(request.user, fields)
try:
renderObj = getAPI.getImageMetadata(imageKey)
except Errors.WebServiceException as e:
renderObj.setError(e)
else:
renderObj.setError(Errors.NO_IMAGE_KEY)
return renderObj
def createTagGroup(request):
imageKey = request.POST.get('imageId', None)
if not imageKey:
raise Errors.MISSING_PARAMETER.setCustom('imageId')
# get the description
name = request.POST.get('name', None)
if not name:
raise Errors.MISSING_PARAMETER.setCustom('name')
# get optional parameter
fields = Util.getDelimitedList(request.POST, 'fields')
postAPI = PostAPI(request.user, fields)
return postAPI.createTagGroup(imageKey, name)
def createTagGroup(request):
imageKey = request.POST.get("imageId", None)
if not imageKey:
raise Errors.MISSING_PARAMETER.setCustom("imageId")
# get the description
name = request.POST.get("name", None)
if not name:
raise Errors.MISSING_PARAMETER.setCustom("name")
# get optional parameter
fields = Util.getDelimitedList(request.POST, "fields")
postAPI = PostAPI(request.user, fields)
return postAPI.createTagGroup(imageKey, name)
def updateTagGroup(request):
# read in the crucial parameters
tagGroupKey = request.PUT.get('id', None)
if not tagGroupKey:
raise Errors.MISSING_PARAMETER.setCustom('id')
name = request.PUT.get('name', None)
# read in optional parameters and initialize the API
fields = Util.getDelimitedList(request.PUT, 'fields')
putAPI = PutAPI(request.user, fields)
if not name:
raise Errors.NOT_MODIFIED
return putAPI.updateTagGroup(tagGroupKey, name)
def addQtl(request):
# get new note information
qtl = request.POST.get('qtl', None)
pq_id = request.POST.get('pq_id', None)
imageKey = request.POST.get('pictureID', None)
print 'test addQql()'
if not imageKey:
raise Errors.NO_IMAGE_KEY
# read in optional parameters and initialize the API
fields = Util.getDelimitedList(request.POST, 'fields')
postAPI = PostAPI(request.user, fields)
return postAPI.addQtl(qtl, pq_id, imageKey)
def updateTagGroup(request):
# read in the crucial parameters
tagGroupKey = request.PUT.get("id", None)
if not tagGroupKey:
raise Errors.MISSING_PARAMETER.setCustom("id")
name = request.PUT.get("name", None)
# read in optional parameters and initialize the API
fields = Util.getDelimitedList(request.PUT, "fields")
putAPI = PutAPI(request.user, fields)
if not name:
raise Errors.NOT_MODIFIED
return putAPI.updateTagGroup(tagGroupKey, name)
def getTag(request):
# read in crucial parameters
tagKey = request.GET.get('id', None)
# read in optional parameters and initialize the API
fields = Util.getDelimitedList(request.GET, 'fields')
getAPI = GetAPI(request.user, fields)
#TEST for debugging - logger
logger = logging.getLogger(__name__)
logger.error('logger test - ktcho')
if not tagKey:
raise Errors.NO_TAG_KEY
# the key for lookup and the image it is attached to
return getAPI.getTag(tagKey)
def createGeneLink(request):
# get tagId for new gene link
tagId = request.POST.get('tagId', None)
if not tagId:
raise Errors.NO_TAG_KEY
name = request.POST.get('name', None)
allele = request.POST.get('allele', None)
organismId = request.POST.get('organismId', None)
# read in optional parameters and initialize the API
fields = Util.getDelimitedList(request.POST, 'fields')
if not (allele or (name and organismId)):
if not allele:
raise Errors.MISSING_PARAMETER.setCustom('allele')
else:
raise Errors.INVALID_SYNTAX.setCustom(
'name and organismId required as a pair')
postAPI = PostAPI(request.user, fields)
return postAPI.createGeneLink(tagId, name, allele, organismId)
def createGeneLink(request):
# get tagId for new gene link
tagId = request.POST.get('tagId', None)
if not tagId:
raise Errors.NO_TAG_KEY
# find name or uniquename
name = request.POST.get('name', None)
uniquename = request.POST.get('uniqueName', None)
organismId = request.POST.get('organismId', None)
# read in optional parameters and initialize the API
fields = Util.getDelimitedList(request.POST, 'fields')
if not (uniquename or (name and organismId)):
if not uniquename:
raise Errors.MISSING_PARAMETER.setCustom('uniquename')
else:
raise Errors.INVALID_SYNTAX.setCustom('name and organismId required as a pair')
postAPI = PostAPI(request.user, fields)
return postAPI.createGeneLink(tagId, name, uniquename, organismId)
def doProcessRender(self, request):
self.addPageletBinding('navBar', NavBarPagelet(addHelpButton=True))
numSearch = 0
searchCats = list('00000')
searchImageDesc = str(request.GET.get('searchImageDesc',
'')).lower() == "true"
searchImageNotes = str(request.GET.get('searchImageNotes',
'')).lower() == "true"
searchGeneName = str(request.GET.get('searchGeneName',
'')).lower() == "true"
searchGeneSymbol = str(request.GET.get('searchGeneSymbol',
'')).lower() == "true"
searchGeneID = str(request.GET.get('searchGeneID',
'')).lower() == "true"
query = Util.getDelimitedList(request.GET, 'query')
if not query:
query = list()
query.append('')
#candidates = [['Image Description'], ['Image Notes'], ['Gene Name'], ['Gene Symbol'], ['Gene ID']]
candidates = [['0'], ['1'], ['2'], ['3'], ['4']]
if searchImageDesc:
candidates[0][0] = 'Image Description'
searchCats[0] = '1'
pictures = Picture.objects.filter(description__icontains=query[0])
for picture in pictures:
candidates[0].append(picture)
if searchImageNotes:
candidates[1][0] = 'Image Notes'
searchCats[1] = '1'
pNotes = PictureNotes.objects.filter(notes__icontains=query[0])
pictureIDs = []
for note in pNotes:
pictureID = note.picture.pk
if not pictureID in pictureIDs:
pictureIDs.append(pictureID)
candidates[1].append(pictureID)
if searchGeneName:
candidates[2][0] = 'Gene Name'
searchCats[2] = '1'
pictureIDs = []
pMgdbs = PictureMgdb.objects.filter(
locus_full_name__icontains=query[0])
for pMgdb in pMgdbs:
pictureID = pMgdb.picture.pk
if not pictureID in pictureIDs:
pictureIDs.append(pictureID)
candidates[2].append(pictureID)
if searchGeneSymbol:
candidates[3][0] = 'Gene Symbol'
searchCats[3] = '1'
pictureIDs = []
pMgdbs = PictureMgdb.objects.filter(locus_name__icontains=query[0])
for pMgdb in pMgdbs:
pictureID = pMgdb.picture.pk
if not pictureID in pictureIDs:
pictureIDs.append(pictureID)
candidates[3].append(pictureID)
if searchGeneID:
candidates[4][0] = 'Gene ID'
searchCats[4] = '1'
pictureIDs = []
pIDs = PictureGeneID.objects.filter(gene_id__icontains=query[0])
for pID in pIDs:
pictureID = pID.picture.pk
if pictureID not in pictureIDs:
pictureIDs.append(pictureID)
candidates[4].append(pictureID)
# Store searching keyword
if str(request.user) != 'AnonymousUser':
catSettings = ''.join(searchCats)
newKeyword, created = iSearchHistory.objects.get_or_create(
keyword=query[0], user=request.user)
if created:
updateKeyword = iSearchHistory.objects.get(
pk__exact=newKeyword.pk)
updateKeyword.catSettings = catSettings
updateKeyword.save()
else:
newKeyword.catSettings = catSettings
newKeyword.save()
formatQuery = ""
if query:
formatQuery += 'General Query: "' + ", ".join(query) + '"'
search = {'candidates': candidates, 'query': query[0]}
numSearch += 1
self.addPageletBinding('center-' + str(numSearch),
iSearchPagelet().setSearchParams(search))
args = {'title': 'Image search', 'numPagelets': numSearch}
self.setApplicationLayout('public/iSearch.html', args)
self.addPageletBinding('footer', FooterPagelet())
def doProcessRender(self, request):
self.addPageletBinding('navBar', NavBarPagelet())
numSearch = 0
searchImages = str(request.GET.get('searchImages', '')).lower() == "true"
searchGenomes = str(request.GET.get('searchGenomes', '')).lower() == "true"
if searchImages or searchGenomes:
query = Util.getDelimitedList(request.GET,'query')
organismId = Util.getDelimitedList(request.GET, 'organismId')
candidates = []
if organismId:
organisms = Organism.objects.filter(pk__in=organismId)
candidates.append(organisms)
if query:
for subquery in query:
splitQuery = subquery.strip().split(' ')
if (len(splitQuery) == 1):
if organismId:
candidate = Organism.objects.filter(species=splitQuery[0]).exclude(organism_id__in=organismId)
else:
candidate = Organism.objects.filter(species=splitQuery[0])
candidates.append(candidate)
elif(len(splitQuery) == 2):
if organismId:
candidate = Organism.objects.filter(Q(species=splitQuery[1]) & Q(genus=splitQuery[0])).exclude(organism_id__in=organismId)
else:
candidate = Organism.objects.filter(Q(species=splitQuery[1]) & Q(genus=splitQuery[0]))
candidates.append(candidate)
else:
if organismId:
candidate = Organism.objects.filter(common_name=subquery).exclude(organism_id__in=organismId)
else:
candidate = Organism.objects.filter(common_name=subquery)
candidates.append(candidate)
formatQuery = ""
if query:
formatQuery += 'General Query: "' + ", ".join(query) + '"'
if organismId:
amp = " & " if query else ""
formatQuery += amp + 'Organism Id Query: "' + ", ".join(organismId) + '"'
search = {
'candidates' : candidates,
'query' : formatQuery
}
if searchImages:
numSearch += 1
self.addPageletBinding('center-' + str(numSearch), ImageSearchPagelet().setSearchParams(search))
if searchGenomes:
numSearch += 1
self.addPageletBinding('center-' + str(numSearch), GBrowseSearchPagelet().setSearchParams(search))
args = {
'title' : 'Search',
'numPagelets' : numSearch
}
self.setApplicationLayout('public/search.html', args)
self.addPageletBinding('footer', FooterPagelet())