def get_job_ids(self, annotation):
job_ids = m_models.AnalysisJobGoTerm.objects \
.filter(
M_Q(go_slim__go_term=annotation) |
M_Q(go_terms__go_term=annotation)
) \
.distinct('job_id')
return job_ids
def get_queryset(self):
lineage = urllib.parse.unquote(
self.kwargs.get('lineage', None).strip())
organism = m_models.Organism.objects \
.filter(lineage=lineage) \
.only('name').distinct('name')
if len(organism) == 0:
raise Http404(("Attribute error '%s'." % self.lookup_field))
queryset = m_models.Organism.objects \
.filter(M_Q(ancestors__in=organism) | M_Q(name__in=organism))
return queryset
def get_queryset(self):
lineage = urllib.parse.unquote(
self.kwargs.get(self.lookup_field, None).strip())
organism = m_models.Organism.objects.filter(lineage=lineage) \
.only('id')
if len(organism) == 0:
raise NotFound("Lineage not found. Lineage: " + lineage)
job_ids = m_models.AnalysisJobTaxonomy.objects \
.filter(
M_Q(taxonomy__organism__in=organism) |
M_Q(taxonomy_lsu__organism__in=organism) |
M_Q(taxonomy_ssu__organism__in=organism)
).distinct('job_id')
return emg_models.AnalysisJob.objects \
.filter(job_id__in=job_ids) \
.available(self.request)
def get_queryset(self): # noqa C901
"""Filter the analysis job contigs
"""
obj = self.get_object()
queryset = m_models.AnalysisJobContig.objects
request = self.request
query_filter = M_Q()
# TODO: simplify!
filter_cog = request.GET.get('cog', '').upper()
if filter_cog:
query_filter |= M_Q(cogs__cog=filter_cog)
filter_kegg = request.GET.get('kegg', '').upper()
if filter_kegg:
query_filter |= M_Q(keggs__ko=filter_kegg)
filter_go = request.GET.get('go', '').upper()
if filter_go:
query_filter |= M_Q(gos__go_term=filter_go)
filter_interpro = request.GET.get('interpro', '').upper()
if filter_interpro:
query_filter |= M_Q(interpros__interpro_identifier=filter_interpro)
filter_pfam = request.GET.get('pfam', '').upper()
if filter_pfam:
query_filter |= M_Q(pfams__pfam_entry=filter_pfam)
filter_antismash = request.GET.get('antismash', '').lower()
if filter_antismash:
query_filter |= M_Q(as_geneclusters__gene_cluster=filter_antismash)
if 'facet[]' in request.GET:
facets = request.GET.getlist('facet[]')
# TODO: try to simplify this
facet_qs = M_Q()
if len(facets):
for facet in [
f for f in facets
if getattr(m_models.AnalysisJobContig, 'has_' +
f, False)
]:
facet_qs |= M_Q(**{'has_' + facet: True})
else:
# contigs with no annotations
for f in m_models.AnalysisJobContig._fields:
if f.startswith('has_'):
facet_qs &= M_Q(**{f: False})
query_filter &= (facet_qs)
len_filter = M_Q()
filter_gt = request.GET.get('gt', None)
filter_lt = request.GET.get('lt', None)
if filter_gt:
len_filter &= M_Q(length__gte=filter_gt)
if filter_lt:
len_filter &= M_Q(length__lte=filter_lt)
if len_filter:
query_filter &= (len_filter)
search = request.GET.get('search', '')
if search:
query_filter &= M_Q(contig_id__icontains=search)
identifier = M_Q(job_id=obj.job_id,
pipeline_version=obj.pipeline.release_version)
return queryset.filter(identifier & query_filter)
def get_job_ids(self, annotation):
return m_models.AnalysisJobKeggOrtholog.objects \
.filter(M_Q(ko_entries__ko=annotation)) \
.distinct('job_id')
def get_job_ids(self, annotation):
return m_models.AnalysisJobAntiSmashGeneCluser.objects \
.filter(M_Q(antismash_gene_clusters__gene_cluster=annotation)) \
.distinct('job_id')
def get_job_ids(self, annotation):
return m_models.AnalysisJobGenomeProperty.objects \
.filter(M_Q(genome_properties__genome_property=annotation)) \
.distinct('job_id')
def get_job_ids(self, annotation):
return m_models.AnalysisJobPfam.objects \
.filter(M_Q(pfam_entries__pfam=annotation)) \
.distinct('job_id')
def get_job_ids(self, annotation):
return m_models.AnalysisJobKeggModule.objects \
.filter(M_Q(kegg_modules__module=annotation)) \
.distinct('job_id')
def get_job_ids(self, annotation):
return m_models.AnalysisJobInterproIdentifier.objects \
.filter(M_Q(interpro_identifiers__interpro_identifier=annotation)) \
.distinct('job_id')