def alignment_view(request, project_uid, alignment_group_uid):
"""View of a single AlignmentGroup.
"""
project = get_object_or_404(Project, owner=request.user.get_profile(),
uid=project_uid)
alignment_group = get_object_or_404(AlignmentGroup,
reference_genome__project=project, uid=alignment_group_uid)
# Initial javascript data.
init_js_data = json.dumps({
'project': adapt_model_instance_to_frontend(project),
'alignment_group': adapt_model_instance_to_frontend(alignment_group)
})
context = {
'project': project,
'tab_root': TAB_ROOT__DATA,
'alignment_group': alignment_group,
'experiment_sample_to_alignment_list_json': adapt_model_to_frontend(
ExperimentSampleToAlignment,
{'alignment_group': alignment_group}),
'init_js_data': init_js_data,
'flag_genome_finishing_enabled': int(settings.FLAG__GENOME_FINISHING_ENABLED)
}
return render(request, 'alignment.html', context)
def alignment_view(request, project_uid, alignment_group_uid):
"""View of a single AlignmentGroup.
"""
project = get_object_or_404(Project, owner=request.user.get_profile(),
uid=project_uid)
alignment_group = get_object_or_404(AlignmentGroup,
reference_genome__project=project, uid=alignment_group_uid)
if request.POST:
return _rerun_alignment(alignment_group)
# Initial javascript data.
init_js_data = json.dumps({
'project': adapt_model_instance_to_frontend(project),
'alignment_group': adapt_model_instance_to_frontend(alignment_group)
})
context = {
'project': project,
'tab_root': TAB_ROOT__DATA,
'alignment_group': alignment_group,
'experiment_sample_to_alignment_list_json': adapt_model_to_frontend(
ExperimentSampleToAlignment,
{'alignment_group': alignment_group}),
'init_js_data': init_js_data
}
return render(request, 'alignment.html', context)
def variant_set_view(request, project_uid, variant_set_uid):
"""Data view for a single VariantSet which includes options for taking
actions on the VariantSet.
"""
project = get_object_or_404(Project, owner=request.user.get_profile(),
uid=project_uid)
variant_set = get_object_or_404(VariantSet,
reference_genome__project=project,
uid=variant_set_uid)
# Initial javascript data.
init_js_data = json.dumps({
'entity': {
'uid': variant_set.uid,
'project': adapt_model_instance_to_frontend(project),
'refGenomeUid': variant_set.reference_genome.uid,
}
})
context = {
'project': project,
'tab_root': TAB_ROOT__DATA,
'variant_set': variant_set,
'init_js_data': init_js_data,
'is_print_mage_oligos_enabled':
settings.FLAG__PRINT_MAGE_OLIGOS_ENABLED,
'is_generate_new_reference_genome_enabled':
settings.FLAG__GENERATE_NEW_REFERENCE_GENOME_ENABLED
}
return render(request, 'variant_set.html', context)
def alignment_create_view(request, project_uid):
"""Displays the view for creating a new alignment.
Also handles POST request to actually creating the alignment.
"""
project = get_object_or_404(Project, owner=request.user.get_profile(),
uid=project_uid)
# Validate and kick off new alignment.
if request.POST:
return _start_new_alignment(request, project)
# Show the data that renders the create view.
init_js_data = json.dumps({
'entity': adapt_model_instance_to_frontend(project)
})
is_new_project = bool(request.GET.get('is_new_project', False))
context = {
'project': project,
'tab_root': TAB_ROOT__DATA,
'init_js_data': init_js_data,
'is_new_project': is_new_project
}
return render(request, 'alignment_create.html', context)
def alignment_create_view(request, project_uid):
"""Displays the view for creating a new alignment.
Also handles POST request to actually creating the alignment.
"""
project = get_object_or_404(Project, owner=request.user.get_profile(),
uid=project_uid)
# Validate and kick off new alignment.
if request.POST:
return _start_new_alignment(request, project)
# Show the data that renders the create view.
init_js_data = json.dumps({
'entity': adapt_model_instance_to_frontend(project)
})
is_new_project = bool(request.GET.get('is_new_project', False))
context = {
'project': project,
'tab_root': TAB_ROOT__DATA,
'init_js_data': init_js_data,
'is_new_project': is_new_project
}
return render(request, 'alignment_create.html', context)
def reference_genome_view(request, project_uid, ref_genome_uid):
"""Overview of a single ReferenceGenome.
"""
project = get_object_or_404(Project, owner=request.user.get_profile(),
uid=project_uid)
reference_genome = ReferenceGenome.objects.get(project=project,
uid=ref_genome_uid)
init_js_data = json.dumps({
'entity': adapt_model_instance_to_frontend(reference_genome)
})
context = {
'project': project,
'tab_root': TAB_ROOT__DATA,
'reference_genome': reference_genome,
'reference_genome_uid': reference_genome.uid,
'has_fasta': reference_genome.dataset_set.filter(
type=Dataset.TYPE.REFERENCE_GENOME_FASTA).exists(),
'has_genbank': reference_genome.dataset_set.filter(
type=Dataset.TYPE.REFERENCE_GENOME_GENBANK).exists(),
'jbrowse_link': reference_genome.get_client_jbrowse_link(),
'init_js_data': init_js_data
}
return render(request, 'reference_genome.html', context)
def reference_genome_view(request, project_uid, ref_genome_uid):
"""Overview of a single project.
"""
project = get_object_or_404(Project, owner=request.user.get_profile(),
uid=project_uid)
reference_genome = ReferenceGenome.objects.get(project=project,
uid=ref_genome_uid)
init_js_data = json.dumps({
'entity': adapt_model_instance_to_frontend(reference_genome)
})
context = {
'project': project,
'tab_root': TAB_ROOT__DATA,
'reference_genome': reference_genome,
'reference_genome_uid': reference_genome.uid,
'has_fasta': reference_genome.dataset_set.filter(
type=Dataset.TYPE.REFERENCE_GENOME_FASTA).exists(),
'has_genbank': reference_genome.dataset_set.filter(
type=Dataset.TYPE.REFERENCE_GENOME_GENBANK).exists(),
'jbrowse_link': reference_genome.get_client_jbrowse_link(),
'init_js_data': init_js_data
}
return render(request, 'reference_genome.html', context)
def variant_set_view(request, project_uid, variant_set_uid):
"""Data view for a single VariantSet which includes options for taking
actions on the VariantSet.
"""
project = get_object_or_404(Project, owner=request.user.get_profile(),
uid=project_uid)
variant_set = get_object_or_404(VariantSet,
reference_genome__project=project,
uid=variant_set_uid)
# Initial javascript data.
init_js_data = json.dumps({
'entity': {
'uid': variant_set.uid,
'project': adapt_model_instance_to_frontend(project),
'refGenomeUid': variant_set.reference_genome.uid,
}
})
context = {
'project': project,
'tab_root': TAB_ROOT__DATA,
'variant_set': variant_set,
'init_js_data': init_js_data,
'is_print_mage_oligos_enabled':
settings.FLAG__PRINT_MAGE_OLIGOS_ENABLED,
'is_generate_new_reference_genome_enabled':
settings.FLAG__GENERATE_NEW_REFERENCE_GENOME_ENABLED
}
return render(request, 'variant_set.html', context)
def tab_root_analyze(request, project_uid, alignment_group_uid=None, sub_view=None):
"""The analyze view. Subviews are loaded in Javascript.
"""
context = {}
project = get_object_or_404(Project, owner=request.user.get_profile(),
uid=project_uid)
# Initial javascript data to establish initial state.
init_js_data = {
'project': adapt_model_instance_to_frontend(project)
}
alignment_group = None
if alignment_group_uid is not None:
alignment_group = get_object_or_404(AlignmentGroup,
uid=alignment_group_uid,
reference_genome__project__owner=request.user.get_profile())
init_js_data['alignmentGroup'] = adapt_model_instance_to_frontend(
alignment_group)
context['active_alignment_group'] = alignment_group
ref_genome = alignment_group.reference_genome
init_js_data['refGenome'] = adapt_model_instance_to_frontend(
ref_genome)
context['active_ref_genome'] = ref_genome
if sub_view is not None:
if not sub_view in VALID_ANALYZE_SUB_VIEWS:
raise Http404
init_js_data['subView'] = sub_view
context['sub_view'] = sub_view
ref_genomes_with_alignments = [
rg for rg in ReferenceGenome.objects.filter(project=project)
if rg.alignmentgroup_set.exists()]
context.update({
'project': project,
'init_js_data': json.dumps(init_js_data),
'tab_root': TAB_ROOT__ANALYZE,
'ref_genomes_with_alignments': ref_genomes_with_alignments,
'genome_finish_enabled': settings.FLAG__GENOME_FINISHING_ENABLED
})
return render(request, 'tab_root_analyze.html', context)
def tab_root_analyze(request, project_uid, alignment_group_uid=None, sub_view=None):
"""The analyze view. Subviews are loaded in Javascript.
"""
context = {}
project = get_object_or_404(Project, owner=request.user.get_profile(),
uid=project_uid)
# Initial javascript data to establish initial state.
init_js_data = {
'project': adapt_model_instance_to_frontend(project)
}
alignment_group = None
if alignment_group_uid is not None:
alignment_group = get_object_or_404(AlignmentGroup,
uid=alignment_group_uid,
reference_genome__project__owner=request.user.get_profile())
init_js_data['alignmentGroup'] = adapt_model_instance_to_frontend(
alignment_group)
context['active_alignment_group'] = alignment_group
ref_genome = alignment_group.reference_genome
init_js_data['refGenome'] = adapt_model_instance_to_frontend(
ref_genome)
context['active_ref_genome'] = ref_genome
if sub_view is not None:
if not sub_view in VALID_ANALYZE_SUB_VIEWS:
raise Http404
init_js_data['subView'] = sub_view
context['sub_view'] = sub_view
ref_genomes_with_alignments = [rg for rg in ReferenceGenome.objects.all()
if rg.alignmentgroup_set.exists()]
context.update({
'project': project,
'init_js_data': json.dumps(init_js_data),
'tab_root': TAB_ROOT__ANALYZE,
'ref_genomes_with_alignments': ref_genomes_with_alignments
})
return render(request, 'tab_root_analyze.html', context)
def variant_set_list_view(request, project_uid):
project = get_object_or_404(Project, owner=request.user.get_profile(),
uid=project_uid)
error_string = ''
# If a POST, then we are creating a new variant set.
if request.method == 'POST':
# Common validation.
# TODO: Most of this should be validated client-side.
if (not 'refGenomeID' in request.POST or
request.POST['refGenomeID'] == ''):
error_string = 'No reference genome selected.'
elif (not 'variantSetName' in request.POST or
request.POST['variantSetName'] == ''):
error_string = 'No variant set name.'
if not error_string:
ref_genome_uid = request.POST['refGenomeID']
variant_set_name = request.POST['variantSetName']
# Handling depending on which form was submitted.
if request.POST['create-set-type'] == 'from-file':
error_string = _create_variant_set_from_file(request, project,
ref_genome_uid, variant_set_name)
elif request.POST['create-set-type'] == 'empty':
error_string = _create_variant_set_empty(project,
ref_genome_uid, variant_set_name)
else:
return HttpResponseBadRequest("Invalid request.")
# Grab all the ReferenceGenomes for this project
# (for choosing which ref genome a new variant set goes into).
ref_genome_list = ReferenceGenome.objects.filter(project=project)
# Initial javascript data.
init_js_data = json.dumps({
'entity': adapt_model_instance_to_frontend(project)
})
context = {
'project': project,
'tab_root': TAB_ROOT__DATA,
'ref_genome_list' : ref_genome_list,
'init_js_data' : init_js_data,
'error_string': error_string
}
return render(request, 'variant_set_list.html', context)
def variant_set_list_view(request, project_uid):
project = get_object_or_404(Project, owner=request.user.get_profile(),
uid=project_uid)
error_string = ''
# If a POST, then we are creating a new variant set.
if request.method == 'POST':
# Common validation.
# TODO: Most of this should be validated client-side.
if (not 'refGenomeID' in request.POST or
request.POST['refGenomeID'] == ''):
error_string = 'No reference genome selected.'
elif (not 'variantSetName' in request.POST or
request.POST['variantSetName'] == ''):
error_string = 'No variant set name.'
if not error_string:
ref_genome_uid = request.POST['refGenomeID']
variant_set_name = request.POST['variantSetName']
# Handling depending on which form was submitted.
if request.POST['create-set-type'] == 'from-file':
error_string = _create_variant_set_from_file(request, project,
ref_genome_uid, variant_set_name)
elif request.POST['create-set-type'] == 'empty':
error_string = _create_variant_set_empty(project,
ref_genome_uid, variant_set_name)
else:
return HttpResponseBadRequest("Invalid request.")
# Grab all the ReferenceGenomes for this project
# (for choosing which ref genome a new variant set goes into).
ref_genome_list = ReferenceGenome.objects.filter(project=project)
# Initial javascript data.
init_js_data = json.dumps({
'entity': adapt_model_instance_to_frontend(project)
})
context = {
'project': project,
'tab_root': TAB_ROOT__DATA,
'ref_genome_list' : ref_genome_list,
'init_js_data' : init_js_data,
'error_string': error_string
}
return render(request, 'variant_set_list.html', context)
def alignment_list_view(request, project_uid):
project = get_object_or_404(Project, owner=request.user.get_profile(),
uid=project_uid)
init_js_data = json.dumps({
'entity': adapt_model_instance_to_frontend(project)
})
context = {
'project': project,
'tab_root': TAB_ROOT__DATA,
'init_js_data': init_js_data,
}
return render(request, 'alignment_list.html', context)
def alignment_list_view(request, project_uid):
project = get_object_or_404(Project, owner=request.user.get_profile(),
uid=project_uid)
init_js_data = json.dumps({
'entity': adapt_model_instance_to_frontend(project)
})
context = {
'project': project,
'tab_root': TAB_ROOT__DATA,
'init_js_data': init_js_data,
}
return render(request, 'alignment_list.html', context)
def project_view(request, project_uid):
"""Overview of a single project.
"""
project = get_object_or_404(Project, owner=request.user.get_profile(),
uid=project_uid)
# Initial javascript data.
init_js_data = json.dumps({
'entity': adapt_model_instance_to_frontend(project)
})
context = {
'project': project,
'init_js_data': init_js_data,
'tab_root': TAB_ROOT__DATA
}
return render(request, 'project.html', context)
def project_view(request, project_uid):
"""Overview of a single project.
"""
project = get_object_or_404(Project, owner=request.user.get_profile(),
uid=project_uid)
# Initial javascript data.
init_js_data = json.dumps({
'entity': adapt_model_instance_to_frontend(project)
})
context = {
'project': project,
'init_js_data': init_js_data,
'tab_root': TAB_ROOT__DATA
}
return render(request, 'project.html', context)
def reference_genome_list_view(request, project_uid):
"""Shows the ReferenceGenomes and handles creating new
ReferenceGenomes when requested.
"""
project = get_object_or_404(Project, owner=request.user.get_profile(),
uid=project_uid)
init_js_data = json.dumps({
'entity': adapt_model_instance_to_frontend(project)
})
context = {
'project': project,
'tab_root': TAB_ROOT__DATA,
'init_js_data': init_js_data,
}
return render(request, 'reference_genome_list.html', context)
def genome_finish_view(request, project_uid):
"""Displays reference genomes on the opening page of
the genome finish tab
"""
project = get_object_or_404(Project, owner=request.user.get_profile(),
uid=project_uid)
init_js_data = json.dumps({
'entity': adapt_model_instance_to_frontend(project)
})
context = {
'project': project,
'tab_root': TAB_ROOT__DATA,
'init_js_data': init_js_data,
}
return render(request, 'genome_finish.html', context)
def reference_genome_list_view(request, project_uid):
"""Shows the ReferenceGenomes and handles creating new
ReferenceGenomes when requested.
"""
project = get_object_or_404(Project, owner=request.user.get_profile(),
uid=project_uid)
init_js_data = json.dumps({
'entity': adapt_model_instance_to_frontend(project)
})
context = {
'project': project,
'tab_root': TAB_ROOT__DATA,
'init_js_data': init_js_data,
}
return render(request, 'reference_genome_list.html', context)
def contig_view(request, project_uid, contig_uid):
"""Overview of a single Contig.
"""
project = get_object_or_404(Project, owner=request.user.get_profile(),
uid=project_uid)
contig = Contig.objects.get(
parent_reference_genome__project=project, uid=contig_uid)
init_js_data = json.dumps({
'entity': adapt_model_instance_to_frontend(contig)
})
context = {
'project': project,
'tab_root': TAB_ROOT__DATA,
'contig': contig,
'init_js_data': init_js_data,
}
return render(request, 'contig.html', context)