def __init__(self, *args, **kwargs):
super(DiffFormRelease, self).__init__(*args, **kwargs)
current_release = ReleaseUtils.get_latest_release()
current_assembly = ReleaseUtils.get_latest_assembly()
default_source = ReleaseUtils.get_default_source()
self.fields['species'] = forms.CharField(widget=forms.Select(
choices=FormUtils.get_all_species_name_tuples()),
required=False)
self.fields['diff_me_assembly'] = forms.CharField(
initial=current_assembly,
widget=forms.Select(choices=FormUtils.get_all_assembly_name_tuples(
))) # @IgnorePep8
self.fields['diff_me_release'] = forms.CharField(
initial=current_release,
widget=forms.Select(choices=FormUtils.get_all_release_name_tuples(
))) # @IgnorePep8
self.fields['diff_with_assembly'] = forms.CharField(
initial=current_assembly,
widget=forms.Select(choices=FormUtils.get_all_assembly_name_tuples(
))) # @IgnorePep8
self.fields['diff_with_release'] = forms.CharField(
initial=int(current_release) - 1,
widget=forms.Select(choices=FormUtils.get_all_release_name_tuples(
))) # @IgnorePep8
self.fields['diff_with_source'] = forms.CharField(
initial=default_source,
widget=forms.Select(
choices=FormUtils.get_all_sources_tuples())) # @IgnorePep8
self.fields['diff_me_source'] = forms.CharField(
initial=default_source,
widget=forms.Select(
choices=FormUtils.get_all_sources_tuples())) # @IgnorePep8
def __init__(self, *args, **kwargs):
super(CompareSetForm, self).__init__(*args, **kwargs)
current_release = ReleaseUtils.get_latest_release()
current_assembly = ReleaseUtils.get_latest_assembly()
current_source = ReleaseUtils.get_default_source()
self.fields['diff_current_assembly'] = forms.CharField(
initial=current_assembly,
widget=forms.Select(choices=FormUtils.get_all_assembly_name_tuples(
))) # @IgnorePep8
self.fields['diff_current_release'] = forms.CharField(
initial=int(current_release),
widget=forms.Select(choices=FormUtils.get_all_release_name_tuples(
source_name="all"))) # @IgnorePep8
self.fields['diff_current_source'] = forms.CharField(
initial=current_source,
widget=forms.Select(
choices=FormUtils.get_all_sources_tuples())) # @IgnorePep8
self.fields['diff_compare_assembly'] = forms.CharField(
initial=current_assembly,
widget=forms.Select(choices=FormUtils.get_all_assembly_name_tuples(
))) # @IgnorePep8
self.fields['diff_compare_release'] = forms.CharField(
initial=int(current_release) - 1,
widget=forms.Select(choices=FormUtils.get_all_release_name_tuples(
source_name="all"))) # @IgnorePep8
self.fields['diff_compare_source'] = forms.CharField(
initial=current_source,
widget=forms.Select(
choices=FormUtils.get_all_sources_tuples())) # @IgnorePep8
def init_assembly_releases(request):
# default is ensembl
all_assembly_releases = json.dumps(
ReleaseUtils.get_all_assembly_releases())
all_assembly_releases_refseq = json.dumps(
ReleaseUtils.get_all_assembly_releases("RefSeq"))
all_assembly_releases_ensembl = json.dumps(
ReleaseUtils.get_all_assembly_releases("Ensembl"))
current_release = ReleaseUtils.get_latest_release()
current_assembly = ReleaseUtils.get_latest_assembly()
source_name = ReleaseUtils.get_default_source()
init_hash = {
"all_assembly_releases": all_assembly_releases,
"all_assembly_releases_ensembl": all_assembly_releases_ensembl,
"all_assembly_releases_refseq": all_assembly_releases_refseq,
"current_release": current_release,
"current_assembly": current_assembly,
"release_name": current_release,
"assembly_name": current_assembly,
'release_name_compare': int(current_release) - 1,
'assembly_name_compare': current_assembly,
'source_name': source_name
}
return init_hash
def init_assembly_releases(request):
# default is ensembl
all_assembly_releases = json.dumps(
ReleaseUtils.get_all_assembly_releases())
all_assembly_releases_refseq = json.dumps(
ReleaseUtils.get_all_assembly_releases("RefSeq"))
all_assembly_releases_ensembl = json.dumps(
ReleaseUtils.get_all_assembly_releases("Ensembl"))
current_release = ReleaseUtils.get_latest_release()
current_assembly = ReleaseUtils.get_latest_assembly()
source_name = ReleaseUtils.get_default_source()
software_release_tag = "1.0.0" if settings.SOFTWARE_RELEASE_TAG is None else settings.SOFTWARE_RELEASE_TAG
init_hash = {
"all_assembly_releases": all_assembly_releases,
"all_assembly_releases_ensembl": all_assembly_releases_ensembl,
"all_assembly_releases_refseq": all_assembly_releases_refseq,
"current_release": current_release,
"current_assembly": current_assembly,
"release_name": current_release,
"assembly_name": current_assembly,
'release_name_compare': int(current_release) - 1,
'assembly_name_compare': current_assembly,
'source_name': source_name,
'software_release_tag': software_release_tag
}
return init_hash
def get_query_params(cls, request, diff_type=None):
params_diff = {}
stable_id_cur = request.query_params.get(diff_type + '_stable_id',
None)
if '.' in stable_id_cur:
stable_id, stable_id_version = stable_id_cur.split('.')
params_diff['stable_id'] = stable_id
params_diff['stable_id_version'] = stable_id_version
else:
params_diff['stable_id'] = request.query_params.get(
diff_type + '_stable_id', None)
params_diff['release_short_name'] = request.query_params.get(
diff_type + '_release', ReleaseUtils.get_latest_release())
params_diff['assembly_name'] = request.query_params.get(
diff_type + '_assembly', ReleaseUtils.get_latest_assembly())
params_diff['source_name'] = request.query_params.get(
diff_type + '_source', ReleaseUtils.get_default_source())
# params_diff['expand'] = request.query_params.get('expand', "transcript_release_set,translations, sequence")
params_diff['expand_all'] = request.query_params.get(
'expand_all', "true")
return params_diff
def test_get_latest_assembly(self):
latest_assembly = ReleaseUtils.get_latest_assembly()
current_assembly = getattr(settings, "CURRENT_ASSEMBLY", "GRCh38")
self.assertEquals(latest_assembly, current_assembly,
"Got the correct latest assembly " + latest_assembly)
def get_queryset(self):
latest_release = self.kwargs['release_name']
latest_assembly = self.kwargs['assembly_name']
latest_source = self.kwargs['source_name']
if latest_release is None:
latest_release = ReleaseUtils.get_latest_release()
if latest_assembly is None:
latest_assembly = ReleaseUtils.get_latest_assembly()
if latest_source is None:
latest_source = ReleaseUtils.get_default_source()
self.unfiltered_query_set = query_set = Transcript.objects.filter(
Q(transcript_release_set__shortname__icontains=latest_release) &
Q(assembly__assembly_name__icontains=latest_assembly) &
Q(transcript_release_set__source__shortname__icontains=latest_source))
order_by_index = int(self.request.query_params.get('order[0][column]', 0))
orderable = bool(self.request.query_params.get('columns[{}][orderable]'.format(order_by_index), 'false'))
if order_by_index == 0 or not orderable:
order_by_index = 1
order_by = self.request.query_params.get('columns[{}][data]'.format(order_by_index), self.default_order_by).\
replace('.', '__')
order_by_dir = self.request.query_params.get('order[0][dir]', 'asc')
if order_by_dir == 'desc':
order_by = '-{}'.format(order_by)
search_queries = self.request.query_params.get('search[value]', '').strip().split(' ')
q = Q()
if len(search_queries) > 0 and search_queries[0] != u'':
for params in self.search_parameters:
if "genes" == params:
for query in search_queries:
temp = {
'{}__hgnc__name__icontains'.format(params): query,
}
q |= Q(**temp)
else:
for query in search_queries:
if not query.isdigit() and params in ["transcript_id", "stable_id_version", "loc_start",
"loc_end"]:
continue
temp = {
'{}__icontains'.format(params): query,
}
q |= Q(**temp)
query_set = query_set.filter(q).distinct()
if order_by == '':
return query_set
return query_set.order_by(order_by)