def search_gene_names(request, key=None):
'''
get: render a form for user to search_gene_names the sequence id for a fasta sequence from a genome.
post: redirect to a page which will show the id.
key: used to pass a message (via the cache)
'''
message = ''
if request.method == 'POST': # If the form has been submitted...
form = SearchGeneNamesForm(request.POST) # A form bound to the POST data
if form.is_valid(): # All validation rules pass
logging.debug(form.cleaned_data)
search_type, query_string = form.cleaned_data['search_type'], form.cleaned_data['query_string']
pairs = roundup_db.findGeneNameGenomePairsLike(
webconfig.CURRENT_RELEASE, substring=query_string,
searchType=search_type)
# store result in cache, so can do a redirect/get.
key = makeUniqueId()
roundup_util.cacheSet(key, {'search_type': search_type, 'query_string': query_string, 'pairs': pairs})
# redirect the post to a get. http://en.wikipedia.org/wiki/Post/Redirect/Get
return django.shortcuts.redirect(django.core.urlresolvers.reverse(search_gene_names_result, kwargs={'key': key}))
else:
if key and roundup_util.cacheHasKey(key):
# a message for the search page can be passed via the cache.
kw = roundup_util.cacheGet(key)
message = kw['message']
form = SearchGeneNamesForm(kw) # A bound form
else:
form = SearchGeneNamesForm() # An unbound form
example = "{'search_type': 'contains', 'query_string': 'ata'}" # javascript
return django.shortcuts.render(request, 'search_gene_names.html', {'message': message, 'form': form, 'nav_id': 'search_gene_names', 'form_doc_id': 'search_gene_names',
'form_action': django.core.urlresolvers.reverse(search_gene_names), 'form_example': example})
def browse(request):
'''
GET: send user the form to make a browse query
POST: validate browse query and REDIRECT to result if it is good.
'''
if request.method == 'POST': # If the form has been submitted...
form = BrowseForm(request.POST) # A form bound to the POST data
if form.is_valid(): # All validation rules pass
logging.debug(u'form.cleaned_data={}'.format(form.cleaned_data))
orthQuery = makeOrthQueryFromBrowseForm(form)
logging.debug(u'orthQuery={}'.format(orthQuery))
# Process and add Browse Ids to the query
# I would rather not have this complexity in here at all. There must be a simpler and more powerful way.
browseId = form.cleaned_data.get('identifier')
browseIdType = form.cleaned_data.get('identifier_type')
logging.debug(u'browseId={}, browseIdType={}'.format(browseId, browseIdType))
if browseId and browseIdType == 'gene_name_type':
genome = form.cleaned_data['primary_genome']
seqIds = roundup_db.getSeqIdsForGeneName(
webconfig.CURRENT_RELEASE, geneName=browseId, genome=genome)
if not seqIds: # no seq ids matching the gene name were found. oh no!
message = u'In your Browse query, Roundup did not find any gene named "{}" in the genome "{}". Try searching for a gene name.'.format(browseId, GENOME_TO_NAME[genome])
# store result in cache, so can do a redirect/get.
key = makeUniqueId()
roundup_util.cacheSet(key, {'message': message, 'search_type': 'contains', 'query_string': browseId})
return django.shortcuts.redirect(django.core.urlresolvers.reverse(search_gene_names, kwargs={'key': key}))
else:
# remake orthQuery with seqIds
form.cleaned_data['seq_ids'] = seqIds
orthQuery = makeOrthQueryFromBrowseForm(form)
elif browseId and browseIdType == 'seq_id_type':
# remake orthQuery with seqIds
form.cleaned_data['seq_ids'] = browseId.split() # split on whitespace
orthQuery = makeOrthQueryFromBrowseForm(form)
# cache the query and redirect to a page that will "get" the query result
queryId = orthQueryHash(orthQuery)
roundup_util.cacheSet(queryId, orthQuery)
return django.shortcuts.redirect(django.core.urlresolvers.reverse(orth_query, kwargs={'queryId': queryId}))
else:
form = BrowseForm(initial={'primary_genome_filter': [value for value, name in CAT_CHOICES],
'secondary_genomes_filter': [value for value, name in CAT_CHOICES]
}) # An unbound form
# example = json.dumps({'primary_genome': '559292', 'identifier': 'Q03834',
# 'identifier_type': 'seq_id_type', 'secondary_genomes': ['9606', '10090']})
example = json.dumps({'primary_genome': 'Drosophila melanogaster',
'identifier': 'Q9VVT2', 'identifier_type': 'seq_id_type',
'secondary_genomes': 'H**o sapiens\nMus musculus\n'})
# example = "{'primary_genome': 'MYCGE', 'secondary_genomes': ['MYCHH', 'MYCH1']}" # javascript
# , 'include_gene_name': 'true', 'include_go_term': 'true'}" # javascript
return django.shortcuts.render(request, 'browse.html',
{'form': form, 'nav_id': 'browse', 'form_doc_id': 'browse', 'chosen_ids': ['id_primary_genome', 'id_secondary_genomes'],
'form_action': django.core.urlresolvers.reverse(browse), 'form_example': example,
'cat_genomes_json': json.dumps(CAT_GENOMES, indent=-1), })
def cluster(request):
'''
GET: send user the form to make a cluster query
POST: validate cluster query and REDIRECT to result if it is good.
'''
if request.method == 'POST': # If the form has been submitted...
form = ClusterForm(request.POST) # A form bound to the POST data
if form.is_valid(): # All validation rules pass
orthQuery = makeOrthQueryFromClusterForm(form)
queryId = orthQueryHash(orthQuery)
roundup_util.cacheSet(queryId, orthQuery)
# cache the query and redirect to a page that will run the query
return django.shortcuts.redirect(django.core.urlresolvers.reverse(orth_query, kwargs={'queryId': queryId}))
else:
form = ClusterForm(initial={'genomes_filter': [value for value, name in CAT_CHOICES]}) # An unbound form
example = json.dumps({'genomes': 'H**o sapiens\nMus musculus\nDrosophila melanogaster\n'})
return django.shortcuts.render(request, 'cluster.html',
{'form': form, 'nav_id': 'cluster', 'form_doc_id': 'cluster', 'chosen_ids': ['id_genomes'],
'form_action': django.core.urlresolvers.reverse(cluster), 'form_example': example,
'cat_genomes_json': json.dumps(CAT_GENOMES, indent=-1), })
def lookup(request):
'''
get: render a form for user to lookup the sequence id for a fasta sequence from a genome.
post: redirect to a page which will show the id.
'''
raise django.http.Http404
if request.method == 'POST': # If the form has been submitted...
form = LookupForm(request.POST) # A form bound to the POST data
if form.is_valid(): # All validation rules pass
logging.debug(form.cleaned_data)
genome, fasta = form.cleaned_data['genome'], form.cleaned_data['fasta']
seqId = BioUtilities.findSeqIdWithFasta(fasta, roundup.dataset.getGenomeIndexPath(webconfig.CURRENT_DATASET, genome))
# store result in cache, so can do a redirect/get.
key = makeUniqueId()
roundup_util.cacheSet(key, {'genome': genome, 'fasta': fasta, 'seqId': seqId})
# redirect the post to a get. http://en.wikipedia.org/wiki/Post/Redirect/Get
return django.shortcuts.redirect(django.core.urlresolvers.reverse(lookup_result, kwargs={'key': key}))
else:
form = LookupForm() # An unbound form
example = "{'fasta': '>example_nameline\\nMNFLWKGRRFLIAGILPTFEGAADEIVDKENKTYKAFLASKPPEETGLERLKQMFTIDEF', 'genome': '7227'}"
return django.shortcuts.render(request, 'lookup.html', {'form': form, 'nav_id': 'lookup', 'form_doc_id': 'lookup',
'form_action': django.core.urlresolvers.reverse(lookup), 'form_example': example})
