def create_library(name,
status=0,
save=True,
read_length=None,
index_type=None):
organism = Organism(name='Organism')
organism.save()
concentration_method = ConcentrationMethod(name='Concentration Method')
concentration_method.save()
if read_length is None:
read_length = ReadLength(name='Read Length')
read_length.save()
library_protocol = LibraryProtocol(
name='Protocol',
type='DNA',
provider='-',
catalog='-',
explanation='-',
input_requirements='-',
typical_application='-',
)
library_protocol.save()
library_type = LibraryType(name='Library Type')
library_type.save()
library_type.library_protocol.add(library_protocol)
if index_type is None:
index_type = IndexType(name='Index Type')
index_type.save()
library = Library(
name=name,
status=status,
organism_id=organism.pk,
concentration=1.0,
concentration_method_id=concentration_method.pk,
read_length_id=read_length.pk,
sequencing_depth=1,
library_protocol_id=library_protocol.pk,
library_type_id=library_type.pk,
amplification_cycles=1,
index_type_id=index_type.pk,
index_reads=0,
mean_fragment_size=1,
)
if save:
library.save()
return library
def post(self, request):
user = User.objects.get(id=request.POST.get('user'))
library = Library()
library.title = request.POST.get('title')
library.save()
library.user.add(user)
return redirect("library:libraries")
def pandora_import(request):
'''Handles post request of pandora username for artists import from
pandora.
'''
form = forms.PandoraUsernameForm(request.POST)
if form.is_valid():
username = form.cleaned_data.get('username')
library = Library(name=username)
library.save()
tasks.import_pandora_artists.delay(library.id, username)
library_id = utils.encrypt_id(library.pk)
return redirect('library_success', library_id)
else:
form = forms.PandoraUsernameForm()
return direct_to_template(request, 'library/upload.html', locals())
def post_form_data(self, request):
'''
Accepts an 'application/x-www-form-urlencoded' post request with
key-value pairs of artist=album and a name=name of library pair
'''
logger.debug('form posted')
data = request.POST
if 'name' in data:
library_name = data['name']
library = Library(name=library_name)
else:
library = Library()
library.save()
tasks.import_form_data.delay(library.pk, data)
return library.pk
def handle(self, *args, **options):
chunk_size = options.get("chunk")
bulk_mngr = BulkCreateManager(chunk_size)
fake = Faker()
for counter in range(self.NO_OF_SEED_LIBRARY):
library = Library(name=fake.name() + " Library",
updated_at=timezone.now(),
archived=False)
bulk_mngr.add(library)
bulk_mngr.done()
library_qs = Library.objects.all()
print("-- Done creating libraries --")
for library in library_qs:
no_of_books_for_library = random.randint(
self.MIN_NO_OF_BOOKS_PER_LIBRARY,
self.MAX_NO_OF_BOOKS_PER_LIBRARY)
print("-- Adding %s books to %s(%s) --" %
(no_of_books_for_library, library.name, library.id))
for counter in range(no_of_books_for_library):
book = Book(title=fake.sentence(),
publisher=fake.company(),
library=library,
updated_at=timezone.now(),
archived=False)
bulk_mngr.add(book)
bulk_mngr.done()
def post_library(self, request):
form = forms.UploadFileForm(request.POST, request.FILES)
if form.is_valid():
library_name = form.cleaned_data.get('name', None)
if library_name == None:
library = Library()
else:
library = Library(name=library_name)
library.save()
library_filename = self._save_library_file(request.FILES['file'])
tasks.import_itunes_file.delay(library.id, library_filename)
return library, None
return None, form
def lastfm_import(request):
'''Handles post request of last.fm username for artists import from
last.fm.
'''
if request.method == 'POST':
form = forms.LastfmUsernameForm(request.POST)
if form.is_valid():
user = form.user
library = Library(name=user.name)
library.save()
tasks.import_lastfm_artists.delay(library.id, user)
library_id = utils.encrypt_id(library.pk)
return redirect('library_success', library_id)
else:
form = forms.LastfmUsernameForm()
return direct_to_template(request, 'test_form.html', {'form': form})
def setUp(self):
user = User.objects.create_user(email='*****@*****.**', password='******')
pool = Pool(name='_Foo', user=user)
pool.save()
library = Library.get_test_library('Library')
library.save()
pool.libraries.add(library)
def setUp(self):
user = User.objects.create_user(email='*****@*****.**', password='******')
pool = Pool(name='_Foo', user=user)
pool.save()
library = Library.get_test_library('Library')
library.save()
pool.libraries.add(library)
def get(self, *args, **kwargs):
session = self.get_session()
page_num = self.get_int_argument('page', 0)
libraries, page_num, page_count = Library.list_by_page(page_num)
return self.render('library/list.html',
session=session,
libraries=libraries,
page_num=page_num,
page_count=page_count)
def post(self, *args, **kwargs):
keyword = self.get_str_argument('keyword', '')
page_num = self.get_int_argument('page')
page_num, page_count, libraries = Library.search_text_by_page(
keyword, page_num)
return self.render('library/search_text_results.html',
libraries=libraries,
keyword=keyword,
page_num=page_num,
page_count=page_count)
def post(self, *args, **kwargs):
search_datas = self.get_json_argument('searchDatas', [])
page_num = self.get_int_argument('page')
libraries, page_num, page_count = Library.search_manual_by_page(
search_datas, page_num)
return self.render('library/search_manual_results.html',
libraries=libraries,
search_datas=search_datas,
page_num=page_num,
page_count=page_count)
def setUp(self):
user = User.objects.create_user(email='*****@*****.**', password='******')
user.save()
self.request = Request(user=user)
self.request.save()
self.library = Library.get_test_library('Library')
self.sample = Sample.get_test_sample('Sample')
self.library.save()
self.sample.save()
def setUp(self):
user = User.objects.create_user(email='*****@*****.**', password='******')
user.save()
self.request = Request(user=user)
self.request.save()
self.library = Library.get_test_library('Library')
self.sample = Sample.get_test_sample('Sample')
self.library.save()
self.sample.save()
def post(self, *args, **kwargs):
library_id = self.get_str_argument('id', '')
title = self.get_str_argument('title', '')
black_player_name = self.get_str_argument('blackPlayerName', '')
white_player_name = self.get_str_argument('whitePlayerName', '')
manual = self.get_json_argument('manual', {})
library = Library.save_and_index(self.current_user,
id=library_id,
title=title,
blackPlayerName=black_player_name,
whitePlayerName=white_player_name,
manual=manual)
return self.api_succeed({'id': str(library.id)})
def setUp(self):
user = User.objects.create_user(email='*****@*****.**', password='******')
pool = Pool(name='_Foo', user=user)
pool.save()
library_1 = Library.get_test_library('Library1')
library_2 = Library.get_test_library('Library2')
library_1.save()
library_2.save()
sample_1 = Sample.get_test_sample('Sample1')
sample_2 = Sample.get_test_sample('Sample2')
sample_1.save()
sample_2.save()
pool.libraries.add(library_1)
pool.samples.add(sample_1)
self.request = Request(user=user)
self.request.save()
self.request.libraries.add(*[library_1, library_2])
self.request.samples.add(*[sample_1, sample_2])
def setUp(self):
user = User.objects.create_user(email='*****@*****.**', password='******')
pool = Pool(name='_Foo', user=user)
pool.save()
library_1 = Library.get_test_library('Library1')
library_2 = Library.get_test_library('Library2')
library_1.save()
library_2.save()
sample_1 = Sample.get_test_sample('Sample1')
sample_2 = Sample.get_test_sample('Sample2')
sample_1.save()
sample_2.save()
pool.libraries.add(library_1)
pool.samples.add(sample_1)
self.request = Request(user=user)
self.request.save()
self.request.libraries.add(*[library_1, library_2])
self.request.samples.add(*[sample_1, sample_2])
def test_get_all_empty(self):
self.client.login(email='*****@*****.**', password='******')
library = Library.get_test_library('Library2')
library.save()
sample = Sample.get_test_sample('Sample2')
sample.save()
self.request.libraries.add(library)
self.request.samples.add(sample)
response = self.client.get(reverse('library.get_all'),
{'quality_check': 'true'})
self.assertEqual(response.status_code, 200)
self.assertEqual(response.content, b'[]')
def test_get_all_empty(self):
self.client.login(email='*****@*****.**', password='******')
library = Library.get_test_library('Library2')
library.save()
sample = Sample.get_test_sample('Sample2')
sample.save()
self.request.libraries.add(library)
self.request.samples.add(sample)
response = self.client.get(reverse('library.get_all'), {
'quality_check': 'true'
})
self.assertEqual(response.status_code, 200)
self.assertEqual(response.content, b'[]')
def render_report_tool_box_function(header: str,
xpath: str,
section: str,
libraries: Library,
instruction: Instruction = None,
library_history: LibraryHistory = None):
split_head = header.split()
guid = xpath[xpath.find('{') +
1:xpath.find('}')] # get guid in xpath between bracket
temp_header = [] # temp for concat each splitted head to final_header
final_header = header
library_history = library_history if library_history else LibraryHistory.objects.filter(
instruction=instruction)
replaced_indexes = set()
skip_amount_loop = 0
if libraries:
libraries = libraries.order_by(Length('key').desc())
for i, head in enumerate(split_head):
if skip_amount_loop == 0:
k = i
library_matched = False
highlight_html = '''
<span class="highlight-library d-inline-block">
<span class="{}">{}</span>
<span class="dropdown-options" data-guid="{}" data-word_idx="{}" data-section="{}">
<a href="#/" class="highlight-redact">Redact</a>
<a href="#/" class="highlight-replace">Replace</a>
<a href="#/" class="highlight-replaceall">Replace all</a>
</span>
</span>
'''
for library in libraries:
step = len(library.key.split(' '))
phrase = " ".join((split_head[k:k + step]))
if str.upper(library.key) == str.upper(
phrase.replace(
',',
'')) and not replaced_indexes.intersection(
set({k, k + step})):
trail = ''
if phrase[
-1] not in string.ascii_letters + string.digits:
trail = phrase[-1]
replace_word = phrase.replace(',', '')
library_matched = True
highlight_class = 'bg-warning'
if not library.value:
highlight_html = '''
<span class="highlight-library d-inline-block">
<span class="{}">{}</span>
<span class="dropdown-options" data-guid="{}" data-word_idx="{}" data-section="{}">
<a href="#/" class="highlight-redact">Redact</a>
</span>
</span>
'''
for history in library_history:
action = history.action
if str.upper(history.old) == str.upper(
phrase.replace(',', '')):
if action == LibraryHistory.ACTION_REPLACE \
and history.guid == guid \
and history.index == i \
and history.section == section:
replace_word = history.new
highlight_class = 'text-danger'
break # already matched HISTORY exist loop
elif action == LibraryHistory.ACTION_HIGHLIGHT_REDACT \
and history.guid == guid \
and history.index == i \
and history.section == section:
highlight_class = 'bg-dark text-dark'
break # already matched HISTORY exist loop
elif action == LibraryHistory.ACTION_REPLACE_ALL:
replace_word = history.new
highlight_class = 'text-danger'
break # already matched HISTORY exist loop
replaced_indexes = replaced_indexes.union(
set(list(range(k, k + step))))
highlight_html = highlight_html.format(
highlight_class, replace_word, guid, i, section)
temp_header.append(highlight_html + trail)
skip_amount_loop = step - 1
break # already matched LIBRARY WORD exist loop
k += 1
if not library_matched:
temp_header.append(head)
else:
skip_amount_loop -= 1
final_header = format_html(" ".join(temp_header))
return final_header
def save(request):
library_form = LibraryForm(request.POST or None)
if library_form.is_valid():
form_clean = library_form.cleaned_data
pk = form_clean.get('id', None)
if not pk:
library_model = Library(**form_clean)
library_model.save()
else:
library_model = get_object_or_404(Library, pk=pk)
library_model.title = form_clean.get('title', '')
library_model.description = form_clean.get('description', '')
library_model.status = form_clean.get('status', '')
library_model.friend_name = form_clean.get('friend_name', '')
library_model.friend_email = form_clean.get('friend_email', '')
library_model.save()
return HttpResponseRedirect(reverse('index'))
book_list = Library.objects.all()
return render(request, 'library/library.html', {'book_list': book_list, 'library_form': library_form})
def setUp(self):
self.library = Library.get_test_library('Library')
self.pooling = Pooling(library=self.library)
