def index(request: HttpRequest, voucher_code: str, gene_code: str) -> HttpResponse:
"""Runs a local blast for voucher code and gene code
Show results to user in a table
"""
blast = BLAST('local', voucher_code, gene_code)
blast.save_seqs_to_file()
if not blast.is_blast_db_up_to_date():
try:
blast.create_blast_db()
except CalledProcessError:
log.warning("there are no sequences for gene %s", gene_code)
was_sequence_saved = blast.save_query_to_file()
if was_sequence_saved:
blast.do_blast()
result = blast.parse_blast_output()
blast.delete_query_output_files()
else:
result = {
"error": "Query sequence has no valid codons, only question marks",
}
context = get_context(request)
context["result"] = result
return render(request, 'blast_local/index.html', context)
def results(request):
context = get_context(request)
if request.method == 'POST':
log.debug(request.POST)
form = BLASTNewForm(request.POST)
if form.is_valid():
cleaned_data = form.cleaned_data
blast = BLASTNew(
blast_type='new',
name=cleaned_data['name'],
sequence=cleaned_data['sequence'],
gene_codes=cleaned_data['gene_codes'],
)
blast.save_seqs_to_file()
if not blast.is_blast_db_up_to_date():
blast.create_blast_db()
blast.save_query_to_file()
blast.do_blast()
result = blast.parse_blast_output()
if not result:
result = None
blast.delete_query_output_files()
context["result"] = result
return render(request, 'blast_new/results.html', context)
else:
context["form"] = form
return render(request, 'blast_new/index.html', context)
return HttpResponseRedirect('/blast_new/')
def index(request: HttpRequest, voucher_code: str,
gene_code: str) -> HttpResponse:
"""Runs a local blast for voucher code and gene code
Show results to user in a table
"""
blast = BLAST('local', voucher_code, gene_code)
blast.save_seqs_to_file()
if not blast.is_blast_db_up_to_date():
try:
blast.create_blast_db()
except CalledProcessError:
log.warning("there are no sequences for gene %s", gene_code)
was_sequence_saved = blast.save_query_to_file()
if was_sequence_saved:
blast.do_blast()
result = blast.parse_blast_output()
blast.delete_query_output_files()
else:
result = {
"error": "Query sequence has no valid codons, only question marks",
}
context = get_context(request)
context["result"] = result
return render(request, 'blast_local/index.html', context)
def show_voucher(request, voucher_code):
context = get_context(request)
try:
voucher_queryset = Vouchers.objects.get(code__iexact=voucher_code)
except Vouchers.DoesNotExist:
raise Http404
flickr_images_queryset = FlickrImages.objects.filter(voucher=voucher_code)
local_images_queryset = LocalImages.objects.filter(voucher=voucher_code)
images_queryset = list(chain(flickr_images_queryset,
local_images_queryset))
seqs_queryset = Sequences.objects.filter(code=voucher_code).values(
'code',
'gene_code',
'number_ambiguous_bp',
'accession',
'lab_person',
'total_number_bp',
)
sorted_seqs_queryset = sorted(seqs_queryset,
key=lambda x: x['gene_code'].lower())
context['voucher'] = voucher_queryset
context['images'] = images_queryset
context['sequences'] = sorted_seqs_queryset
context['google_maps_api_key'] = settings.GOOGLE_MAPS_API_KEY
return render(request, 'public_interface/show_voucher.html', context)
def results(request, dataset_id):
context = get_context(request)
try:
dataset = Dataset.objects.get(id=dataset_id)
except Dataset.DoesNotExist:
raise Http404(f'such dataset {dataset_id} does not exist')
if dataset.sister_dataset_id:
aa_dataset = dataset
try:
nucleotide_dataset = Dataset.objects.get(
id=aa_dataset.sister_dataset_id)
except Dataset.DoesNotExist:
raise Http404(f'such dataset {dataset_id} does not exist')
else:
nucleotide_dataset = dataset
aa_dataset = None
if aa_dataset:
context['aa_dataset'] = aa_dataset
context['nucleotide_dataset'] = nucleotide_dataset
return render(request, 'create_dataset/results_bankit.html', context)
else:
context['dataset'] = nucleotide_dataset
return render(request, 'create_dataset/results.html', context)
def results(request):
context = get_context(request)
if request.method == 'POST':
log.debug(request.POST)
form = BLASTNewForm(request.POST)
if form.is_valid():
cleaned_data = form.cleaned_data
blast = BLASTNew(
blast_type='new',
name=cleaned_data['name'],
sequence=cleaned_data['sequence'],
gene_codes=cleaned_data['gene_codes'],
)
blast.save_seqs_to_file()
if not blast.is_blast_db_up_to_date():
blast.create_blast_db()
blast.save_query_to_file()
blast.do_blast()
result = blast.parse_blast_output()
if not result:
result = None
blast.delete_query_output_files()
context["result"] = result
return render(request, 'blast_new/results.html', context)
else:
context["form"] = form
return render(request, 'blast_new/index.html', context)
return HttpResponseRedirect('/blast_new/')
def show_voucher(request, voucher_code):
context = get_context(request)
try:
voucher_queryset = Vouchers.objects.get(code__iexact=voucher_code)
except Vouchers.DoesNotExist:
raise Http404
flickr_images_queryset = FlickrImages.objects.filter(voucher=voucher_code)
local_images_queryset = LocalImages.objects.filter(voucher=voucher_code)
images_queryset = list(chain(flickr_images_queryset, local_images_queryset))
seqs_queryset = Sequences.objects.filter(code=voucher_code).values(
'code',
'gene_code',
'number_ambiguous_bp',
'accession',
'lab_person',
'total_number_bp',
)
sorted_seqs_queryset = sorted(seqs_queryset, key=lambda x: x['gene_code'].lower())
context['voucher'] = voucher_queryset
context['images'] = images_queryset
context['sequences'] = sorted_seqs_queryset
context['google_maps_api_key'] = settings.GOOGLE_MAPS_API_KEY
return render(request, 'public_interface/show_voucher.html', context)
def search(request):
"""Simple search tool"""
context = get_context(request)
context['simple_query'] = get_simple_query(request)
if 'q' not in request.GET:
return redirect('/')
query = request.GET['q'].strip()
if query == '':
return redirect('/')
form = SearchForm(request.GET)
page = request.GET.get('page')
if settings.ELASTICSEARCH is True:
sqs = form.search()
sqs.spelling_suggestion()
results = ""
paginator = ""
if sqs:
paginator = Paginator(sqs, 25)
try:
results = paginator.page(page)
except PageNotAnInteger:
# If page is not an integer, deliver first page.
results = paginator.page(1)
except EmptyPage:
# If page is out of range (e.g. 9999), deliver last page of results.
results = paginator.page(paginator.num_pages)
context['page'] = results
context['paginator'] = paginator
context['results'] = results
context['voucher_code_list'] = get_voucher_code_list(sqs)
context['url_encoded_query'] = get_correct_url_query(
request.GET.urlencode())
context['result_count'] = len(sqs)
return render(request, 'public_interface/search_results.html', context)
else:
sqs = Vouchers.objects.filter(
Q(orden__icontains=query) | Q(genus__icontains=query)
| Q(species__icontains=query) | Q(code__icontains=query), )
results = ""
paginator = ""
if sqs:
paginator = Paginator(sqs, 25)
try:
results = paginator.page(page)
except PageNotAnInteger:
# If page is not an integer, deliver first page.
results = paginator.page(1)
except EmptyPage:
# If page is out of range (e.g. 9999), deliver last page of results.
results = paginator.page(paginator.num_pages)
context["result_count"] = sqs.count()
context['page'] = results
context['paginator'] = paginator
context['results'] = results
return render(request, 'public_interface/search_results.html', context)
def results(request):
context = get_context(request)
if request.method == 'POST':
form = GeneTableForm(request.POST)
if form.is_valid():
table = GeneTable(form.cleaned_data)
response = create_excel_file(table.stats)
return response
context["form"] = GeneTableForm()
return render(request, 'gene_table/index.html', context)
def results(request):
context = get_context(request)
if request.method == 'POST':
form = GeneTableForm(request.POST)
if form.is_valid():
table = GeneTable(form.cleaned_data)
response = create_excel_file(table.stats)
return response
context["form"] = GeneTableForm()
return render(request, 'gene_table/index.html', context)
def index(request: HttpRequest, voucher_code: str, gene_code: str) -> HttpResponse:
"""Executes blast of sequence against NCBI genbank"""
blast = BLASTNcbi(blast_type="remote", voucher_code=voucher_code,
gene_code=gene_code)
blast.save_query_to_file()
blast.do_blast()
result = blast.parse_blast_output()
blast.delete_query_output_files()
context = get_context(request)
context["result"] = result
return render(request, 'blast_local/index.html', context)
def index(request: HttpRequest, voucher_code: str, gene_code: str) -> HttpResponse:
"""Executes blast of sequence against NCBI genbank"""
blast = BLASTNcbi(blast_type="remote", voucher_code=voucher_code,
gene_code=gene_code)
blast.save_query_to_file()
blast.do_blast()
result = blast.parse_blast_output()
blast.delete_query_output_files()
context = get_context(request)
context["result"] = result
return render(request, 'blast_local/index.html', context)
def results(request):
context = get_context(request)
if request.method == 'POST':
form = GenBankFastaForm(request.POST)
if form.is_valid():
cleaned_data = form.cleaned_data
cleaned_data['file_format'] = 'GenBankFASTA'
cleaned_data['number_genes'] = ''
cleaned_data['translations'] = False
cleaned_data['aminoacids'] = False
cleaned_data['positions'] = 'ALL'
cleaned_data['partition_by_positions'] = 'by gene'
cleaned_data['taxon_names'] = ['CODE', 'GENUS', 'SPECIES']
cleaned_data['outgroup'] = ''
dataset_creator = CreateDataset(cleaned_data)
dataset = dataset_creator.dataset_str
dataset_short = dataset[
0:
1500] + '\n...\n\n\n' + '#######\nComplete dataset file available for download.\n#######' # noqa
errors = dataset_creator.errors
warnings = dataset_creator.warnings
dataset_file_abs = dataset_creator.dataset_file
items_with_accession = dataset_creator.sequences_skipped
if dataset_file_abs is not None:
dataset_file = os.path.basename(dataset_file_abs)
else:
dataset_file = False
cleaned_data['aminoacids'] = True
dataset_creator = CreateDataset(cleaned_data)
aa_dataset = dataset_creator.dataset_str
aa_dataset_file_abs = dataset_creator.dataset_file
if aa_dataset_file_abs is not None:
aa_dataset_file = os.path.basename(aa_dataset_file_abs)
else:
aa_dataset_file = False
context['items_with_accession'] = items_with_accession
context['dataset'] = dataset_short
context['fasta_file'] = dataset_file
context['protein'] = aa_dataset
context['errors'] = errors
context['protein_file'] = aa_dataset_file
context['warnings'] = warnings
return render(request, 'genbank_fasta/results.html', context)
else:
context["form"] = form
return render(request, 'genbank_fasta/index.html', context)
return HttpResponseRedirect('/genbank_fasta/')
def results(request):
context = get_context(request)
if request.method == 'POST':
form = VoucherTableForm(request.POST)
if form.is_valid():
table = VoucherTable(form.cleaned_data)
response = table.create_csv_file()
return response
else:
context["form"] = form
return render(request, 'voucher_table/index.html', context)
return HttpResponseRedirect('/create_voucher_table/')
def results(request):
context = get_context(request)
if request.method == 'POST':
form = GenBankFastaForm(request.POST)
if form.is_valid():
cleaned_data = form.cleaned_data
cleaned_data['file_format'] = 'GenBankFASTA'
cleaned_data['number_genes'] = ''
cleaned_data['translations'] = False
cleaned_data['aminoacids'] = False
cleaned_data['positions'] = 'ALL'
cleaned_data['partition_by_positions'] = 'by gene'
cleaned_data['taxon_names'] = ['CODE', 'GENUS', 'SPECIES']
cleaned_data['outgroup'] = ''
dataset_creator = CreateDataset(cleaned_data)
dataset = dataset_creator.dataset_str
dataset_short = dataset[0:1500] + '\n...\n\n\n' + '#######\nComplete dataset file available for download.\n#######' # noqa
errors = dataset_creator.errors
warnings = dataset_creator.warnings
dataset_file_abs = dataset_creator.dataset_file
items_with_accession = dataset_creator.sequences_skipped
if dataset_file_abs is not None:
dataset_file = os.path.basename(dataset_file_abs)
else:
dataset_file = False
cleaned_data['aminoacids'] = True
dataset_creator = CreateDataset(cleaned_data)
aa_dataset = dataset_creator.dataset_str
aa_dataset_file_abs = dataset_creator.dataset_file
if aa_dataset_file_abs is not None:
aa_dataset_file = os.path.basename(aa_dataset_file_abs)
else:
aa_dataset_file = False
context['items_with_accession'] = items_with_accession
context['dataset'] = dataset_short
context['fasta_file'] = dataset_file
context['protein'] = aa_dataset
context['errors'] = errors
context['protein_file'] = aa_dataset_file
context['warnings'] = warnings
return render(request, 'genbank_fasta/results.html', context)
else:
context["form"] = form
return render(request, 'genbank_fasta/index.html', context)
return HttpResponseRedirect('/genbank_fasta/')
def search_advanced(request):
"""Uses the haystack index `advanced_search` to find values based on a
combination of queries for one or more fields.
Works in a similar way to **genus:Mopho AND species:helenor**
:param request: HTTP request from the url dispatcher.
:return: response to html template.
"""
context = get_context(request)
if request.method == 'GET' and bool(request.GET) is not False:
form = AdvancedSearchForm(request.GET)
page = request.GET.get('page')
if form.is_valid():
sqs = form.search()
results = ""
paginator = ""
if sqs:
paginator = Paginator(sqs, 25)
try:
results = paginator.page(page)
except PageNotAnInteger:
# If page is not an integer, deliver first page.
results = paginator.page(1)
except EmptyPage:
# If page is out of range (e.g. 9999), deliver last page of results.
results = paginator.page(paginator.num_pages)
if sqs is not None:
context['page'] = results
context['paginator'] = paginator
context['results'] = results
context['voucher_code_list'] = get_voucher_code_list(sqs)
context['simple_query'] = get_simple_query(request)
context['url_encoded_query'] = get_correct_url_query(
request.GET.urlencode())
context['result_count'] = len(sqs)
return render(request, 'public_interface/search_results.html',
context)
else:
context["form"] = form
return render(request, 'public_interface/search_results.html',
context)
else:
context["form"] = form
return render(request, 'public_interface/search.html', context)
else:
form = AdvancedSearchForm()
context["form"] = form
return render(request, 'public_interface/search.html', context)
def generate_results(request):
context = get_context(request)
if request.method == 'POST':
form = CreateDatasetForm(request.POST)
if form.is_valid():
dataset_obj_id = schedule_dataset(form.cleaned_data, request.user)
return HttpResponseRedirect(
reverse('create-dataset-results',
kwargs={'dataset_id': dataset_obj_id}))
else:
log.debug("invalid form")
context["form"] = form
return render(request, 'create_dataset/index.html', context)
def browse(request):
context = get_context(request)
queryset = Vouchers.objects.order_by('-modified')[:10]
vouchers_with_images = []
# Lookups that span relationships
# https://docs.djangoproject.com/en/1.8/topics/db/queries/#lookups-that-span-relationships
for i in Vouchers.objects.filter(flickrimages__voucher_id__isnull=False):
vouchers_with_images.append(i.code)
for i in Vouchers.objects.filter(localimages__voucher_id__isnull=False):
vouchers_with_images.append(i.code)
context["results"] = queryset
context['vouchers_with_images'] = set(vouchers_with_images)
return render(request, 'public_interface/browse.html', context)
def browse(request):
context = get_context(request)
queryset = Vouchers.objects.order_by('-modified')[:10]
vouchers_with_images = []
# Lookups that span relationships
# https://docs.djangoproject.com/en/1.8/topics/db/queries/#lookups-that-span-relationships
for i in Vouchers.objects.filter(flickrimages__voucher_id__isnull=False):
vouchers_with_images.append(i.code)
for i in Vouchers.objects.filter(localimages__voucher_id__isnull=False):
vouchers_with_images.append(i.code)
context["results"] = queryset
context['vouchers_with_images'] = set(vouchers_with_images)
return render(request, 'public_interface/browse.html', context)
def index(request: HttpRequest, voucher_code: str, gene_code: str
) -> HttpResponse:
"""Execute a blast of sequence against all sequences in the database"""
blast = BLASTFull('full', voucher_code, gene_code)
blast.save_seqs_to_file()
if not blast.is_blast_db_up_to_date():
blast.create_blast_db()
blast.save_query_to_file()
blast.do_blast()
result = blast.parse_blast_output()
blast.delete_query_output_files()
context = get_context(request)
context['result'] = result
return render(request, 'blast_local/index.html', context)
def index(request: HttpRequest, voucher_code: str, gene_code: str
) -> HttpResponse:
"""Execute a blast of sequence against all sequences in the database"""
blast = BLASTFull('full', voucher_code, gene_code)
blast.save_seqs_to_file()
if not blast.is_blast_db_up_to_date():
blast.create_blast_db()
blast.save_query_to_file()
blast.do_blast()
result = blast.parse_blast_output()
blast.delete_query_output_files()
context = get_context(request)
context['result'] = result
return render(request, 'blast_local/index.html', context)
def search_advanced(request):
"""Uses the haystack index `advanced_search` to find values based on a
combination of queries for one or more fields.
Works in a similar way to **genus:Mopho AND species:helenor**
:param request: HTTP request from the url dispatcher.
:return: response to html template.
"""
context = get_context(request)
if request.method == 'GET' and bool(request.GET) is not False:
form = AdvancedSearchForm(request.GET)
page = request.GET.get('page')
if form.is_valid():
sqs = form.search()
results = ""
paginator = ""
if sqs:
paginator = Paginator(sqs, 25)
try:
results = paginator.page(page)
except PageNotAnInteger:
# If page is not an integer, deliver first page.
results = paginator.page(1)
except EmptyPage:
# If page is out of range (e.g. 9999), deliver last page of results.
results = paginator.page(paginator.num_pages)
if sqs is not None:
context['page'] = results
context['paginator'] = paginator
context['results'] = results
context['voucher_code_list'] = get_voucher_code_list(sqs)
context['simple_query'] = get_simple_query(request)
context['url_encoded_query'] = get_correct_url_query(request.GET.urlencode())
context['result_count'] = len(sqs)
return render(request, 'public_interface/search_results.html', context)
else:
context["form"] = form
return render(request, 'public_interface/search_results.html', context)
else:
context["form"] = form
return render(request, 'public_interface/search.html', context)
else:
form = AdvancedSearchForm()
context["form"] = form
return render(request, 'public_interface/search.html', context)
def index(request):
context = get_context(request)
voucher_count = get_voucher_count()
queryset = Genes.objects.all().values()
result = []
for i in queryset:
gene_code = i['gene_code']
try:
i['voucher_count'] = voucher_count[gene_code]
except KeyError:
continue
result.append(i)
result = sorted(result, key=lambda k: k['gene_code'].lower())
context["result"] = result
return render(request, 'view_genes/index.html', context)
def index(request):
context = get_context(request)
voucher_count = get_voucher_count()
queryset = Genes.objects.all().values()
result = []
for i in queryset:
gene_code = i['gene_code']
try:
i['voucher_count'] = voucher_count[gene_code]
except KeyError:
continue
result.append(i)
result = sorted(result, key=lambda k: k['gene_code'].lower())
context["result"] = result
return render(request, 'view_genes/index.html', context)
def show_sequence(request, voucher_code, gene_code):
context = get_context(request)
try:
queryset = Vouchers.objects.get(code__iexact=voucher_code)
except Vouchers.DoesNotExist:
raise Http404
seqs_queryset = Sequences.objects.get(code=voucher_code, gene_code=gene_code)
images_queryset = FlickrImages.objects.filter(voucher=voucher_code)
primers_queryset = Primers.objects.filter(for_sequence=seqs_queryset)
context['voucher'] = queryset
context['sequence'] = seqs_queryset
context['images'] = images_queryset
context['primers'] = primers_queryset
return render(request, 'public_interface/show_sequence.html', context)
def search(request):
"""Simple search tool"""
context = get_context(request)
if 'q' not in request.GET:
return redirect('/')
query = request.GET['q'].strip()
if query == '':
return redirect('/')
form = SearchForm(request.GET)
page = request.GET.get('page')
if settings.ELASTICSEARCH is True:
sqs = form.search()
sqs.spelling_suggestion()
results = ""
paginator = ""
if sqs:
paginator = Paginator(sqs, 25)
try:
results = paginator.page(page)
except PageNotAnInteger:
# If page is not an integer, deliver first page.
results = paginator.page(1)
except EmptyPage:
# If page is out of range (e.g. 9999), deliver last page of results.
results = paginator.page(paginator.num_pages)
context['page'] = results
context['paginator'] = paginator
context['results'] = results
context['voucher_code_list'] = get_voucher_code_list(sqs)
context['simple_query'] = get_simple_query(request)
context['url_encoded_query'] = get_correct_url_query(request.GET.urlencode())
context['result_count'] = len(sqs)
return render(request, 'public_interface/search_results.html', context)
else:
sqs = Vouchers.objects.filter(
Q(genus__icontains=query) | Q(species__icontains=query) | Q(code__icontains=query),
)
context["result_count"] = len(sqs)
context["page"] = {'object_list': sqs}
return render(request, 'public_interface/search_results.html', context)
def show_sequence(request, voucher_code, gene_code):
context = get_context(request)
try:
queryset = Vouchers.objects.get(code__iexact=voucher_code)
except Vouchers.DoesNotExist:
raise Http404
seqs_queryset = Sequences.objects.filter(
code=voucher_code, gene__gene_code=gene_code).first()
images_queryset = FlickrImages.objects.filter(voucher=voucher_code)
primers_queryset = Primers.objects.filter(for_sequence=seqs_queryset)
context['voucher'] = queryset
context['sequence'] = seqs_queryset
context['images'] = images_queryset
context['primers'] = primers_queryset
return render(request, 'public_interface/show_sequence.html', context)
def gene(request, gene_code):
context = get_context(request)
queryset = Genes.objects.filter(gene_code=gene_code)
if not queryset:
item = ''
else:
item = queryset[0]
if ';' in item.intron:
introns = item.intron.split(';')
j = 1
out = ''
for i in introns:
out += '<b>Intron ' + str(j) + ':</b> ' + i + ' > '
j += 1
item.intron = out.rstrip(' > ')
context["item"] = item
return render(request, 'view_genes/gene.html', context)
def index(request):
context = get_context(request)
genes = Genes.objects.all().order_by('gene_code')
vouchers = OverviewTable.objects.all()
paginator = Paginator(vouchers, 100)
page = request.GET.get('page')
try:
vouchers_for_page = paginator.page(page)
except PageNotAnInteger:
vouchers_for_page = paginator.page(1)
except EmptyPage:
vouchers_for_page = paginator.page(paginator.num_pages)
context["data"] = vouchers_for_page
context["genes"] = genes
context["page_range"] = paginator.page_range
return render(request, 'overview_table/index.html', context)
def results(request, dataset_id):
context = get_context(request)
try:
aa_dataset = Dataset.objects.get(id=dataset_id)
except Dataset.DoesNotExist:
raise Http404(f'such dataset {dataset_id} does not exist')
try:
nucleotide_dataset = Dataset.objects.get(
id=aa_dataset.sister_dataset_id
)
except Dataset.DoesNotExist:
raise Http404(f'such dataset {dataset_id} does not exist')
context['errors'] = list(nucleotide_dataset.errors or []) + list(aa_dataset.errors or [])
context['warnings'] = list(nucleotide_dataset.warnings or []) + list(aa_dataset.warnings or [])
context['nucleotide_dataset'] = nucleotide_dataset
context['aa_dataset'] = aa_dataset
return render(request, 'genbank_fasta/results.html', context)
def gene(request, gene_code):
context = get_context(request)
queryset = Genes.objects.filter(gene_code=gene_code)
if not queryset:
item = ''
else:
item = queryset[0]
if ';' in item.intron:
introns = item.intron.split(';')
j = 1
out = ''
for i in introns:
out += '<b>Intron ' + str(j) + ':</b> ' + i + ' > '
j += 1
item.intron = out.rstrip(' > ')
context["item"] = item
return render(request, 'view_genes/gene.html', context)
def show_voucher(request, voucher_code):
context = get_context(request)
try:
voucher_queryset = Vouchers.objects.get(code__iexact=voucher_code)
except Vouchers.DoesNotExist:
raise Http404
flickr_images_queryset = FlickrImages.objects.filter(voucher=voucher_code)
local_images_queryset = LocalImages.objects.filter(voucher=voucher_code)
images_queryset = list(chain(flickr_images_queryset,
local_images_queryset))
seqs_queryset = Sequences.objects.filter(
code=voucher_queryset).order_by('gene__gene_code')
context['voucher'] = voucher_queryset
context['images'] = images_queryset
context['sequences'] = seqs_queryset
context['google_maps_api_key'] = settings.GOOGLE_MAPS_API_KEY
return render(request, 'public_interface/show_voucher.html', context)
def results(request):
context = get_context(request)
if request.method == 'POST':
form = CreateDatasetForm(request.POST)
if form.is_valid():
dataset_format = form.cleaned_data['file_format']
dataset_creator = CreateDataset(form.cleaned_data)
dataset = "{}{}{}".format(
dataset_creator.dataset_str[0:1500],
'\n...\n\n\n',
'#######\nComplete dataset file available for download.\n#######',
)
errors = dataset_creator.errors
warnings = set(dataset_creator.warnings)
dataset_file_abs = dataset_creator.dataset_file
if dataset_file_abs is not None:
dataset_file = re.search(
'([A-Z]+_[a-z0-9]+\.txt)',
dataset_file_abs
).groups()[0]
else:
dataset_file = False
context['dataset_file'] = dataset_file
context['charset_block'] = dataset_creator.charset_block
context['dataset'] = dataset
context['dataset_format'] = dataset_format
context['errors'] = errors
context['warnings'] = warnings
return render(request, 'create_dataset/results.html', context)
else:
log.debug("invalid form")
context["form"] = form
return render(request, 'create_dataset/index.html', context)
else:
return HttpResponseRedirect('/create_dataset/')
def results(request):
context = get_context(request)
if request.method == 'POST':
form = CreateDatasetForm(request.POST)
if form.is_valid():
dataset_format = form.cleaned_data['file_format']
dataset_creator = CreateDataset(form.cleaned_data)
dataset = "{}{}{}".format(
dataset_creator.dataset_str[0:1500],
'\n...\n\n\n',
'#######\nComplete dataset file available for download.\n#######',
)
errors = dataset_creator.errors
warnings = set(dataset_creator.warnings)
dataset_file_abs = dataset_creator.dataset_file
if dataset_file_abs is not None:
dataset_file = re.search('([A-Z]+_[a-z0-9]+\.txt)',
dataset_file_abs).groups()[0]
else:
dataset_file = False
context['dataset_file'] = dataset_file
context['charset_block'] = dataset_creator.charset_block
context['dataset'] = dataset
context['dataset_format'] = dataset_format
context['errors'] = errors
context['warnings'] = warnings
return render(request, 'create_dataset/results.html', context)
else:
log.debug("invalid form")
context["form"] = form
return render(request, 'create_dataset/index.html', context)
else:
return HttpResponseRedirect('/create_dataset/')
def index(request):
form = CreateDatasetForm()
context = get_context(request)
context["form"] = form
return render(request, 'create_dataset/index.html', context)
def index(request):
context = get_context(request)
return render(request, 'gbif/index.html', context)
def index(request):
context = get_context(request)
return render(request, 'public_interface/index.html', context)
def index(request):
form = CreateDatasetForm()
context = get_context(request)
context["form"] = form
return render(request, 'create_dataset/index.html', context)
def index(request):
form = BLASTNewForm()
context = get_context(request)
context["form"] = form
return render(request, 'blast_new/index.html', context=context)
def index(request):
form = GenBankFastaForm()
context = get_context(request)
context["form"] = form
return render(request, 'genbank_fasta/index.html', context)
def index(request):
form = BLASTNewForm()
context = get_context(request)
context["form"] = form
return render(request, 'blast_new/index.html', context=context)
def index(request):
form = GenBankFastaForm()
context = get_context(request)
context["form"] = form
return render(request, 'genbank_fasta/index.html', context)
def index(request):
context = get_context(request)
return render(request, 'public_interface/index.html', context)
def index(request):
context = get_context(request)
context["form"] = VoucherTableForm()
return render(request, 'voucher_table/index.html', context)
def index(request):
form = GeneTableForm()
context = get_context(request)
context["form"] = form
return render(request, 'gene_table/index.html', context)
def index(request):
form = GeneTableForm()
context = get_context(request)
context["form"] = form
return render(request, 'gene_table/index.html', context)
