def diff_home(request):
"""
View function for diff query page
"""
# Render the HTML template index.html with data in the context variable
diff_result = {}
diff_release = False
if request.method == 'POST':
form = DiffForm(request.POST)
if form.is_valid():
form_data_dict = form.get_cleaned_data()
transcript_diff_url = ApiUtils.get_feature_diff_url(request, "transcript", form_data_dict)
response = requests.get(transcript_diff_url)
if response.status_code == 200:
diff_result = response.json()
# print(diff_result)
return render(request, 'diff_compare_result.html',
context={'form': form,
'diff_result': diff_result,
'diff_release': diff_release,
'form_data_dict': form_data_dict})
else:
logger.error(form.errors)
else:
form = DiffForm()
return render(request, 'tark_diff.html', context={'form': form,
'diff_release': diff_release,
})
def search_home(request):
"""
View function for search query page
"""
host_url = ApiUtils.get_host_url(request)
search_identifier = ""
query_url = "/api/transcript/search/?expand=transcript_release_set,genes,translations&identifier_field="
# Render the HTML template index.html with data in the context variable
search_result = {}
if request.method == 'GET' and "identifier" in request.GET:
search_identifier = request.GET['identifier']
if search_identifier is not None:
# replace white space
search_identifier = search_identifier.replace(" ", "")
search_form = SearchForm(request.GET)
query_url = query_url + search_identifier
response = requests.get(host_url + query_url)
if response.status_code == 200:
search_result = response.json()
return render(request,
'search_result.html',
context={
'form': search_form,
'search_result': search_result,
'search_identifier': search_identifier
})
else:
logger.error("Error from search")
else:
search_form = SearchForm()
elif request.method == 'POST':
search_form = SearchForm(request.POST)
if search_form.is_valid():
search_identifier = search_form.cleaned_data['search_identifier']
# replace white space
search_identifier = search_identifier.replace(" ", "")
query_url = query_url + search_identifier
response = requests.get(host_url + query_url)
if response.status_code == 200:
search_result = response.json()
return render(request,
'search_result.html',
context={
'form': search_form,
'search_result': search_result,
'search_identifier': search_identifier
})
else:
logger.error("Error from search")
else:
logger.error(search_form.errors)
else:
search_form = SearchForm()
return render(request, 'tark_search.html', context={'form': search_form})
def search_link(request, search_identifier):
search_form = SearchForm(request.POST)
host_url = ApiUtils.get_host_url(request)
query_url = "/api/transcript/search/?identifier_field=" + search_identifier + \
"&expand=transcript_release_set,genes,translations"
response = requests.get(host_url + query_url)
if response.status_code == 200:
search_result = response.json()
return render(request, 'search_result.html', context={'form': search_form,
'search_result': search_result,
'search_identifier': search_identifier})
def transcript_details(request, stable_id_with_version, search_identifier):
host_url = ApiUtils.get_host_url(request)
# get transcript details
query_url_details = "/api/transcript/stable_id_with_version/?stable_id_with_version=" + stable_id_with_version + \
"&expand_all=true"
response = requests.get(host_url + query_url_details)
transcript_details = {}
if response.status_code == 200:
search_result = response.json()
if "results" in search_result and len(search_result["results"]) > 0:
transcript_details = search_result["results"][0]
if "genes" in transcript_details:
gene = transcript_details["genes"][0]
gene_name = gene["name"]
lrg_id = SearchUtils.get_lrg_id_from_hgnc_name(gene_name)
if lrg_id is not None:
gene["lrg_id"] = lrg_id
transcript_details["gene"] = gene
else:
logger.error("Error")
# get transcript history
transcript_history = {}
if '.' in stable_id_with_version:
(identifier, identifier_version) = stable_id_with_version.split(
'.') # @UnusedVariable
query_url_history = "/api/transcript/?stable_id=" + identifier + \
"&expand=transcript_release_set"
response = requests.get(host_url + query_url_history)
if response.status_code == 200:
search_result = response.json()
if "results" in search_result:
transcript_history = search_result["results"]
return render(request,
'transcript_details.html',
context={
'transcript_details': transcript_details,
'transcript_history': transcript_history,
'search_identifier': search_identifier,
'stable_id_with_version': stable_id_with_version
})
def fetch_fasta_sequence(cls,
request,
feature_type,
stable_id,
stable_id_version,
release_short_name=None,
assembly_name=None,
source_name=None,
output_format="fasta"):
if source_name is not None:
source_name = source_name.lower()
host_url = ApiUtils.get_host_url(request)
query_url = ""
if release_short_name is not None and assembly_name is not None and source_name is not None:
query_url = "/api/" + feature_type.lower() + "/?stable_id=" + stable_id + \
"&stable_id_version=" + stable_id_version + \
"&release_short_name=" + release_short_name + \
"&assembly_name=" + assembly_name + \
"&source_name=" + source_name + \
"&expand=sequence"
else:
query_url = "/api/" + feature_type.lower() + "/?stable_id=" + stable_id + \
"&stable_id_version=" + stable_id_version + \
"&expand=sequence"
sequence = None
response = requests.get(host_url + query_url)
if response.status_code == 200:
response_result = response.json()
if "results" in response_result and len(
response_result["results"]) > 0:
sequence_result = response_result["results"][0]
sequence = sequence_result["sequence"]["sequence"]
if sequence and "fasta" in output_format:
id_a = stable_id + '.' + stable_id_version
formatted_seq = cls.format_fasta(sequence, id_=id_a)
return formatted_seq
elif sequence and "raw" in output_format:
return sequence
return sequence
def test_get_host_url(self):
# Create an instance of a GET request.
request = self.factory.get('/api')
host_url = ApiUtils.get_host_url(request)
self.assertEqual("http://testserver", host_url,
"Got the testserver url")
def fetch_cds_sequence(cls,
request,
feature_type,
stable_id,
stable_id_version,
release_short_name=None,
assembly_name=None,
source_name=None,
seq_type="cds",
output_format="raw"):
if source_name is not None:
source_name = source_name.lower()
host_url = ApiUtils.get_host_url(request)
query_url = ""
if release_short_name is not None and assembly_name is not None and source_name is not None:
query_url = "/api/" + feature_type.lower() + "/?stable_id=" + stable_id + \
"&stable_id_version=" + stable_id_version + \
"&release_short_name=" + release_short_name + \
"&assembly_name=" + assembly_name + \
"&source_name=" + source_name + "&expand_all=true"
else:
query_url = "/api/" + feature_type.lower() + "/?stable_id=" + stable_id + \
"&stable_id_version=" + stable_id_version + \
"&expand_all=true"
sequence = None
response = requests.get(host_url + query_url)
if response.status_code == 200:
response_result = response.json()
if "results" in response_result and len(
response_result["results"]) > 0:
transcript_result = response_result["results"][0]
if "translations" in transcript_result and len(
transcript_result["translations"]) > 0:
translation = transcript_result["translations"][0]
if "translation_id" in translation:
tl_translation_id = translation["translation_id"]
tl_query_set = Translation.objects.filter(
translation_id=tl_translation_id).select_related(
'sequence')
if tl_query_set is not None and len(tl_query_set) == 1:
tl_obj = tl_query_set[0]
translation["sequence"] = tl_obj.sequence.sequence
translation[
"seq_checksum"] = tl_obj.sequence.seq_checksum
transcript_result["translations"] = translation
if "exons" in transcript_result:
all_exons = transcript_result["exons"]
new_exons = []
for exon in all_exons:
if "exon_id" in exon:
current_exon_query_set = Exon.objects.filter(
exon_id=exon["exon_id"]
).select_related(
'sequence') # @IgnorePep8
if current_exon_query_set is not None and len(
current_exon_query_set) == 1:
current_exon_with_sequence = current_exon_query_set[
0]
exon[
"sequence"] = current_exon_with_sequence.sequence.sequence
exon[
"seq_checksum"] = current_exon_with_sequence.sequence.seq_checksum
new_exons.append(exon)
if len(new_exons) > 0:
transcript_result["exons"] = new_exons
cds_info = ExonUtils.fetch_cds_info(
transcript_result)
if cds_info:
if seq_type == "cds":
if "cds_seq" in cds_info:
sequence = cds_info['cds_seq']
elif seq_type == "five_prime":
if "five_prime_utr_seq" in cds_info:
sequence = cds_info[
'five_prime_utr_seq']
elif seq_type == "three_prime":
if "three_prime_utr_seq" in cds_info:
sequence = cds_info[
'three_prime_utr_seq']
if output_format == "raw":
return sequence
elif output_format == "fasta":
id_version = stable_id + '.' + stable_id_version
formatted_seq = cls.format_fasta(sequence, id_=id_version)
return formatted_seq
return sequence
def get_search_results(self, request, diff_query_params, attach_translation_seq=True, attach_exon_seq=True,
attach_gene=True, attach_mane=True, attach_cds=True):
host_url = ApiUtils.get_host_url(request)
query_url = "/api/transcript/?"
query_param_string = RequestUtils.get_query_param_string(diff_query_params)
query_url = query_url + query_param_string
response = requests.get(host_url + query_url)
if response.status_code == 200:
search_result = response.json()
if search_result is not None and "count" in search_result and search_result["count"] == 1 and "results" in search_result:
search_result = search_result["results"][0]
if "transcript_release_set" in search_result:
for release_set in search_result["transcript_release_set"]:
if "release_short_name" in diff_query_params and "shortname" in release_set:
if diff_query_params["release_short_name"] == release_set["shortname"]:
search_result["transcript_release_set"] = release_set
# handle mane
if attach_mane is True:
pass
if attach_translation_seq is True:
if "translations" in search_result and len(search_result["translations"]) > 0:
translation = search_result["translations"][0]
if "translation_id" in translation:
tl_translation_id = translation["translation_id"]
tl_query_set = Translation.objects.filter(translation_id=tl_translation_id).select_related('sequence')
if tl_query_set is not None and len(tl_query_set) == 1:
tl_obj = tl_query_set[0]
translation["sequence"] = tl_obj.sequence.sequence
translation["seq_checksum"] = tl_obj.sequence.seq_checksum
search_result["translations"] = translation
if attach_exon_seq is True:
if "exons" in search_result:
all_exons = search_result["exons"]
new_exons = []
for exon in all_exons:
if "exon_id" in exon:
current_exon_query_set = Exon.objects.filter(exon_id=exon["exon_id"]).select_related('sequence') # @IgnorePep8
if current_exon_query_set is not None and len(current_exon_query_set) == 1:
current_exon_with_sequence = current_exon_query_set[0]
exon["sequence"] = current_exon_with_sequence.sequence.sequence
exon["seq_checksum"] = current_exon_with_sequence.sequence.seq_checksum
new_exons.append(exon)
if len(new_exons) > 0:
search_result["exons"] = new_exons
if attach_gene is True:
if "genes" in search_result:
gene = search_result["genes"][0]
search_result["gene"] = gene
if attach_cds is True:
if "translations" in search_result and len(search_result['translations']) > 0:
cds_info = ExonUtils.fetch_cds_info(search_result)
if cds_info:
search_result["cds_info"] = cds_info
return search_result