def test_query_seqs_display(self):
"""
Tests the query sequences display page
"""
# User visits home page and submits a protein alignment
self.client.get(self.url)
csrftoken = self.client.cookies["csrftoken"]
alignment_string = file_to_string("spa_protein_alignment.fasta")
self.client.headers.update({"referer": self.url})
r = self.client.post(
self.url, data={"csrfmiddlewaretoken": csrftoken, "seq_type": "Protein", "align_input": alignment_string}
)
display = html.parse(StringIO(r.text)).getroot()
title = display.cssselect('title[id="head-title"]')
sequence_lines = display.cssselect('p[class="query_seq_display"]')
sequence_meta = display.find_class("query_seq_meta")
render_form = display.cssselect('form[id="render"]')
# She is redirected to a page showing the submitted sequences from her alignment and a simple consensus sequence
self.assertEqual(r.status_code, 200, r.status_code)
self.assertEqual(
"%s/query-sequences" % self.url, "/".join(r.url.split("/")[:-2]), "/".join(r.url.split("/")[:-2])
)
self.assertEqual("Formalign.eu Sequence Display", title[0].text_content(), title[0].text_content())
self.assertIsNotNone(sequence_lines, "sequences are empty")
for l in sequence_lines:
self.assertTrue(len(l.text_content()) <= 80, l.text_content())
seqs = file_to_string("spa_protein_alignment_display.txt").splitlines()
for i, a in enumerate(seqs):
self.assertEqual(
a, sequence_lines[i].text_content(), "%s: %s" % (format(i), sequence_lines[i].text_content())
)
seqs_meta = file_to_string("spa_protein_alignment_display_meta.txt").splitlines()
for i, a in enumerate(seqs_meta):
self.assertEqual(a, sequence_meta[i].text_content(), sequence_meta[i].text_content())
# She is happy with the result, sees a "Render" button and clicks it.
self.assertEqual("get", render_form[0].attrib.get("method"), render_form[0].attrib.get("method"))
self.assertEqual(
"align-display",
render_form[0].attrib.get("action").split("/")[1],
render_form[0].attrib.get("action").split("/")[1],
)
slug_pattern = re.compile("^([a-zA-Z]|\d){16}$")
self.assertTrue(
re.match(slug_pattern, render_form[0].attrib.get("action").split("/")[-2]),
render_form[0].attrib.get("action").split("/")[-2],
)
r = self.client.get(self.url + render_form[0].attrib.get("action"))
# She is redirected to the render page
self.assertEqual(r.status_code, 200, r.status_code)
align = html.parse(StringIO(r.text)).getroot()
title = align.cssselect('title[id="head-title"]')
self.assertEqual("Formalign.eu Alignment Display", title[0].text_content(), title[0].text_content())
self.assertEqual(
"%s/align-display" % self.url, "/".join(r.url.split("/")[:-2]), "/".join(r.url.split("/")[:-2])
)
def setUp(self):
"""
Creates an alignment from ser_thr_kin_short in the db
"""
align_input = io.StringIO(file_to_string("ser_thr_kin_short.fasta"))
data = parse_fasta_alignment(align_input)
for d in data:
d.seq.alphabet = Gapped(ExtendedIUPACProtein())
self.alignment = data
align_input_a = io.StringIO(file_to_string("protein_annotate_test.fasta"))
data_a = parse_fasta_alignment(align_input_a)
for d in data_a:
d.seq.alphabet = Gapped(ExtendedIUPACProtein())
self.alignment_a = data_a
def setUp(self):
name = "A. tha. SPA family protein alignment"
align_input = io.StringIO(file_to_string("spa_protein_alignment.fasta"))
data = parse_fasta_alignment(align_input)
for d in data:
d.seq.alphabet = Gapped(ExtendedIUPACProtein())
align = Alignment.objects.create_alignment(name, data)
self.response_prot = self.client.get("/query-sequences/" + str(align.slug) + "/")
name = "A. tha. SPA family DNA alignment"
align_input = io.StringIO(file_to_string("spa_cds_alignment.fasta"))
data = parse_fasta_alignment(align_input)
for d in data:
d.seq.alphabet = Gapped(ExtendedIUPACDNA())
align = Alignment.objects.create_alignment(name, data)
self.response_dna = self.client.get("/query-sequences/" + str(align.slug) + "/")
def test_form_validation_returns_correct_seqrecord_alphabet(self):
"""
Tests that seqrecords get correct alphabet according to user input of seq_type
:return:
"""
input_seqs = file_to_string('protein.fasta')
form = QueryForm(data={'align_input': input_seqs, 'seq_type': 'Protein'})
self.assertTrue(form.is_valid())
for f in form.cleaned_data['align_input']:
self.assertEqual(str(f.seq.alphabet), "Gapped(ExtendedIUPACProtein(), '-')", Gapped(ExtendedIUPACProtein()).letters)
input_seqs = file_to_string('DNA.fasta')
form = QueryForm(data={'align_input': input_seqs, 'seq_type': 'DNA'})
self.assertTrue(form.is_valid())
for f in form.cleaned_data['align_input']:
self.assertEqual(str(f.seq.alphabet), "Gapped(ExtendedIUPACDNA(), '-')", Gapped(ExtendedIUPACDNA()).letters)
def test_alignment_display_speeds(self):
"""
Tests alignment display page
"""
# User visits home page, submits a protein alignment and renders it
files = [
'spa_protein_alignment.fasta',
'spa1_protein_alignment.fasta',
'ser_thr_kinase_family.fasta'
]
for f in files:
q_display = []
a_display = []
for i in range(3):
self.client = requests.Session()
self.client.get(self.live_server_url)
csrftoken = self.client.cookies['csrftoken']
alignment_string = file_to_string(f)
start = time.time()
r = self.client.post(self.live_server_url,
data={'csrfmiddlewaretoken': csrftoken, 'seq_type': 'Protein',
'align_input': alignment_string})
roundtrip1 = time.time() - start
q_display.append(roundtrip1)
render_form = html.parse(StringIO(r.text)).getroot().cssselect('form[id="render"]')
start = time.time()
r = self.client.get(self.live_server_url + render_form[0].attrib.get('action'))
roundtrip2 = time.time() - start
a_display.append(roundtrip2)
self.client.close()
self.assertTrue(mean(q_display) <= 2, 'query sequences display of %s took: %s' % (f, mean(q_display)))
self.assertTrue(mean(a_display) <= 2, 'alignment display of %s took: %s' % (f, mean(a_display)))
def test_align_display_page_displays_correct_consensus(self):
"""
Tests that align_display displays the correct consensus sequence
"""
expected_seqs = file_to_string("spa_protein_alignment.fasta")
align_expected = io.StringIO(expected_seqs)
alignment = parse_fasta_alignment(align_expected)
alignment = consensus_add(alignment)
# get displayed sequences
with self.assertHTML(self.response, "tr") as elems:
seq_disp = []
for els in elems:
seq_disp_line = []
for e in els.findall("td")[:-1]:
if e.attrib["class"] in ["residue S0", "residue S1"]:
seq_disp_line.append(e.text)
if seq_disp_line:
seq_disp.append(seq_disp_line)
# recompose sequences
cat_re_seq = []
for j in range(len(alignment) - 1, len(seq_disp), len(alignment)):
re_seq = [seq_disp[j] for j in range(len(alignment) - 1, len(seq_disp), len(alignment))]
cat_re_seq = []
for r in re_seq:
cat_re_seq.extend(r)
# check consensus
cons_li = list(alignment[-1].seq)
self.assertEqual(cons_li, cat_re_seq, cat_re_seq)
def test_align_display_page_displays_correct_protein_alignment_sequence(self):
"""
Tests that align_display displays an alignment with correct sequences
"""
expected_seqs = file_to_string("spa_protein_alignment.fasta")
align_expected = io.StringIO(expected_seqs)
alignment = parse_fasta_alignment(align_expected)
# get displayed sequences
with self.assertHTML(self.response, "tr") as elems:
seq_disp = []
for els in elems:
seq_disp_line = []
for e in els.findall("td")[:-1]:
if e.attrib["class"] in ["residue S0", "residue S1"]:
seq_disp_line.append(e.text)
if seq_disp_line:
seq_disp.append(seq_disp_line)
# recompose sequences
re_seqs = []
cat_re_seq = []
for i in range(0, len(alignment) + 1):
for j in range(i, len(seq_disp), len(alignment) + 1):
re_seq = [seq_disp[j] for j in range(i, len(seq_disp), len(alignment) + 1)]
cat_re_seq = []
for r in re_seq:
cat_re_seq.extend(r)
re_seqs.append(cat_re_seq)
# check sequences against original alignment
for i, al in enumerate(alignment):
al_li = list(al.seq)
self.assertEqual(al_li, re_seqs[i], re_seqs[i])
def test_redirect_to_seqdisplay_on_post(self):
"""
Tests that valid POST request on index page redirects to /query-sequences/
:return:
"""
input_seqs = file_to_string("spa_protein_alignment.fasta")
response = self.client.post("/", {"align_input": input_seqs, "seq_type": "Protein"})
self.assertTrue("/query-sequences/" in response.url)
def setUp(self):
self.name = 'A. tha. SPA family alignment'
align_input = io.StringIO(file_to_string('spa_protein_alignment.fasta'))
self.data = parse_fasta_alignment(align_input)
alphabet = Gapped(ExtendedIUPACProtein())
for a in self.data:
a.seq.alphabet = alphabet
self.data._alphabet = alphabet
def test_display_page_uses_display_seq_template(self):
"""
Tests that seq_display view returns a 200 response on a POST request and uses the correct template
:return:
"""
input_seqs = file_to_string("protein.fasta")
response = self.client.post("/", {"align_input": input_seqs, "seq_type": "DNA"})
self.assertEqual(response.status_code, 200)
def setUp(self):
name = 'A. tha. SPA family protein alignment'
align_input = io.StringIO(file_to_string('spa_protein_alignment.fasta'))
data = parse_fasta_alignment(align_input)
for d in data:
d.seq.alphabet = Gapped(ExtendedIUPACProtein())
align = Alignment.objects.create_alignment(name, data)
self.slug = align.slug
def test_alignment_is_saved_on_post(self):
"""
Tests that alignment is saved on valid POST request to index
:return:
"""
input_seqs = file_to_string("spa_protein_alignment.fasta")
response = self.client.post("/", {"align_input": input_seqs, "seq_type": "Protein"})
slug = re.match(r"^/query-sequences/(?P<align_id>([a-zA-Z]|\d){16})/", response.url).group("align_id")
pk = Alignment.objects.get(slug=slug).pk
alignment = Alignment.objects.get_alignment(pk)
self.assertEqual([seq.id for seq in alignment], ["NP_175717", "NP_683567", "NP_182157", "NP_192849"])
def test_parse_fasta_alignment_returns_expected_object(self):
"""
tests that parse_fasta_alignment returns the expected object
"""
align = io.StringIO(file_to_string("ser_thr_kin_short.fasta"))
parsed = parse_fasta_alignment(align)
self.assertEqual(
["DMD401_1-640", "CER09D1_11-435", "EGFR", "DMDPR2_1-384"],
[p.description for p in parsed],
[p.description for p in parsed],
)
def test_parse_fasta_alignment(self):
"""
Tests that the parse_fasta function returns expected values with a valid fasta alignment
:return:
"""
input_seqs = file_to_string("protein.fasta")
parsed = parse_fasta_alignment(io.StringIO(input_seqs))
self.assertEqual(parsed[0].description, "sequence1")
self.assertEqual(parsed[0].seq, "MKERBGWAQ--QGKKPWRF--EEW")
self.assertEqual(parsed[1].description, "sequence2")
self.assertEqual(parsed[1].seq, "MKERBGWA-SYQGKKPWRFAQ-EW")
def setUp(self):
"""
Creates a response from a GET request to /align-display/ with an alignment pk
:param input_file: file containing alignment
:return: response
"""
name = "SPA1 protein alignment"
align_input = io.StringIO(file_to_string("spa1_protein_alignment.fasta"))
data = parse_fasta_alignment(align_input)
for d in data:
d.seq.alphabet = Gapped(ExtendedIUPACProtein())
self.align = Alignment.objects.create_alignment(name, data)
def response_for_invalid_post_request(self, input_file="", seq_type="Protein"):
"""
Creates a response from a POST request to /query-sequences/ with an invalid alignment
:param input_file: file containing invalid alignment
:return: response
"""
if input_file:
input_seqs = file_to_string(input_file)
else:
input_seqs = ""
response = self.client.post("/", {"align_input": input_seqs, "seq_type": seq_type})
return response
def test_display_page_uses_display_seq_template_on_GET(self):
"""
Tests that seq_display view returns a 200 response on a GET request and uses the correct template
:return:
"""
name = "A. tha. SPA family alignment"
align_input = io.StringIO(file_to_string("spa_protein_alignment.fasta"))
data = parse_fasta_alignment(align_input)
for d in data:
d.seq.alphabet = Gapped(ExtendedIUPACProtein())
save = Alignment.objects.create_alignment(name, data)
response = self.client.get("/query-sequences/" + str(save.slug) + "/")
self.assertEqual(response.status_code, 200)
def setUp(self):
seq_input = io.StringIO(file_to_string('spa_protein_alignment.fasta'))
data = SeqIO.parse(seq_input, 'fasta')
self.seqs = [d.upper() for d in data]
for s in self.seqs:
s.seq.alphabet = ExtendedIUPACProtein()
self.seq = Seqrecord.objects.create(
seq=str(self.seqs[0].seq),
alphabet=str(self.seqs[0].seq.alphabet),
seq_id=str(self.seqs[0].id),
name=str(self.seqs[0].name),
description=self.seqs[0].description,
)
def test_display_page_displays_consensus(self):
"""
Tests that seq_display displays the consensus sequence on a valid POST request
:return:
"""
response = self.response_prot
with self.assertHTML(response, 'h3[class="query_seq_meta bg-color-body"]') as elems:
self.assertEqual(elems[-1].text, "consensus 70%:", "consensus meta: " + format(elems[0].text))
cons_seq = file_to_string("consensus.txt")
with self.assertHTML(response, 'div[class="query_seq bg-color-body"]') as elems:
self.assertEqual(
elems[-1].findall("p")[0].text, cons_seq[:80], "consensus seq: " + elems[-1].findall("p")[0].text
)
self.assertNotIn(" ", elems[-1].findall("p")[0].text)
self.assertNotIn("\n", elems[-1].findall("p")[0].text)
def validation(self, error_text, input_file='', seq_type='Protein'):
"""
Performs validation test for invalid forms, takes a user alignment input, asserts form.is_valid as false and
checks the error
:param:
:return:
"""
if input_file:
input_seqs = file_to_string(input_file)
else:
input_seqs = ''
form = QueryForm(data={'align_input': input_seqs, 'seq_type': seq_type})
self.assertFalse(form.is_valid())
self.assertEqual(
form.errors['align_input'],
[error_text], format(form.errors['align_input'])
)
def test_align_display_page_displays_sequences_in_the_correct_order(self):
"""
Tests that align_display displays the sequences in the correct order
"""
expected_seqs = file_to_string("spa_protein_alignment.fasta")
align_expected = io.StringIO(expected_seqs)
alignment = parse_fasta_alignment(align_expected)
ids = [al.id for al in alignment]
ids.append("consensus 70%")
with self.assertHTML(self.response, "tr") as elems:
ids_disp = []
for els in elems:
for e in els.findall("td")[:-1]:
if e.attrib["class"] == "seq_id":
ids_disp.append(e.text)
# blocks of sequence IDs
bl = [ids_disp[i : i + len(ids)] for i in range(0, len(ids_disp), len(ids))]
for b in bl:
for i in range(len(ids)):
self.assertEqual(ids[i], b[i], b[i])
def alignment_validation(self, seqs):
# She visits the Formalign.eu site
r = self.client.get(self.url)
csrftoken = self.client.cookies['csrftoken']
index = html.parse(StringIO(r.text)).getroot()
title = index.cssselect('title[id="head-title"]')
brand = index.cssselect('a[class="navbar-brand"]')
# page displays no error message
self.assertEqual(r.status_code, 200, r.status_code)
# User sees she's on the right page because she can see the name of the site in the title and the brand.
self.assertEqual('Formalign.eu Home', title[0].text_content(), title[0].text_content())
self.assertEqual(self.url + '/', r.url, r.url)
self.assertEqual('Formalign.eu', brand[0].text_content(), brand[0].text_content())
for t in ['protein', 'DNA']:
for s in seqs:
# she submits the invalid alignment
alignment_string = file_to_string('%s%s.fasta' % (t, s['seq'])) if s['seq'] else None
self.client.headers.update({'referer': self.url})
r = self.client.post(self.url,
data={'csrfmiddlewaretoken': csrftoken, 'seq_type': 'Protein',
'align_input': alignment_string})
index = html.parse(StringIO(r.text)).getroot()
title = index.cssselect('title[id="head-title"]')
brand = index.cssselect('a[class="navbar-brand"]')
error_text = index.cssselect('ul[class="errorlist"]')[0].cssselect('li')[0].text_content()
# response contains no error code
self.assertEqual(r.status_code, 200, r.status_code)
# user is redirected to the index page
self.assertEqual('Formalign.eu Home', title[0].text_content(), title[0].text_content())
self.assertEqual(self.url + '/', r.url, r.url)
self.assertEqual('Formalign.eu', brand[0].text_content(), brand[0].text_content())
# error text is displayed on index page
self.assertEqual(s['error'], error_text, error_text)
def test_align_display_renders_correct_color_classes(self):
"""
Tests that align_display assigns the correct color classes (residue S0 or residue S1) to the residues
"""
expected_seqs = file_to_string("spa_protein_alignment.fasta")
align_expected = io.StringIO(expected_seqs)
alignment = parse_fasta_alignment(align_expected)
alignment = consensus_add(alignment)
alignment = annotate(alignment)
# get displayed sequences
with self.assertHTML(self.response, "tr") as elems:
seq_disp = []
for els in elems:
seq_disp_line = []
for e in els.findall("td")[:-1]:
if e.attrib["class"] in ["residue S0", "residue S1"]:
seq_disp_line.append(e.attrib["class"])
if seq_disp_line:
seq_disp.append(seq_disp_line)
# recompose sequences
re_seqs = []
cat_re_seq = []
for i in range(0, len(alignment)):
for j in range(i, len(seq_disp), len(alignment)):
re_seq = [seq_disp[j] for j in range(i, len(seq_disp), len(alignment))]
cat_re_seq = []
for r in re_seq:
cat_re_seq.extend(r)
re_seqs.append(cat_re_seq)
# check color classes
for i, al in enumerate(alignment):
al_li = ["residue S%s" % a for a in al.letter_annotations["eq"]]
self.assertEqual(al_li, re_seqs[i], re_seqs)
def invalid_format_sequence(self, file):
seq_type_button_dict = {'DNA': 'input#id_seq_type_1', 'protein': 'input#id_seq_type_0'}
test_seq = {'DNA': 'AGTCC-TAAGGTCGCCAATGGGCA', 'protein': 'MKERBGWAQ--QGKKPWRF--EEW'}
# she visits the Formalign.eu site
self.browser.get(self.url + '/')
# She clicks the appropriate button and clears the input field
seq_type_button = self.browser.find_element_by_css_selector(seq_type_button_dict[file['seq_type']])
seq_type_button.click()
self.assertEqual(
True,
seq_type_button.is_selected(),
'button is selected for ' + file['align_format'] + ' ' + file['seq_type'] + ': ' +
str(seq_type_button.is_selected())
)
alignment_input = self.browser.find_element_by_css_selector('textarea#id_align_input')
alignment_input.clear()
# She pastes in an invalid fasta alignment
alignment_string = file_to_string(file['invalid'])
pyperclip.copy(alignment_string)
alignment_input.send_keys(Keys.CONTROL, 'v')
self.browser.find_element_by_id('submit-align').click()
# Wait for Firefox
time.sleep(self.wait)
# Since her FASTA format is invalid she gets redirected to the submission form where she sees an
# error message telling her that her alignment format is invalid
self.assertEqual(
'Formalign.eu Home',
self.browser.title,
'browser.title for ' + file['align_format'] + ' ' + file['seq_type'] + ': ' + self.browser.title
)
error = self.browser.find_element_by_css_selector('.errorlist').find_element_by_tag_name('li')
self.assertEqual(
FORMAT_ERROR,
error.text,
'error.text for ' + file['align_format'] + ' ' + file['seq_type'] + ': ' + error.text,
)
# she corrects her alignment and submits an invalid clustal alignment
alignment_input = self.browser.find_element_by_css_selector('textarea#id_align_input')
alignment_input.clear()
alignment_string = file_to_string(file['valid'])
pyperclip.copy(alignment_string)
alignment_input.send_keys(Keys.CONTROL, 'v')
self.browser.find_element_by_id('submit-align').click()
# Wait for Firefox
time.sleep(self.wait * 10)
# She got it right this time and is redirected to a page showing the submitted sequences from her alignment
self.assertEqual(
'Formalign.eu Sequence Display',
self.browser.title,
'browser.title for ' + file['align_format'] + ' ' + file['seq_type'] + ': ' + self.browser.title)
first_seq_info = self.browser.find_elements_by_css_selector('.query_seq_meta')[0]
self.assertEqual(
'sequence1:',
first_seq_info.text,
'seq id for ' + file['align_format'] + ' ' + file['seq_type'] + ': ' + first_seq_info.text
)
first_seq_content = self.browser.find_elements_by_css_selector('.query_seq_display')[0]
self.assertIsNotNone(first_seq_content)
self.assertEqual(
test_seq[file['seq_type']],
first_seq_content.text,
'seq id for ' + file['align_format'] + ' ' + file['seq_type'] + ': ' + first_seq_content.text
)
# She wonders whether she can use other formats and decides to navigate back to the home page
home_button = self.browser.find_element_by_css_selector('.navbar-brand')
home_button.click()
def alignment_validation(self, **kwargs):
seq_type_button_dict = {'DNA': 'input#id_seq_type_1', 'protein': 'input#id_seq_type_0'}
test_seq = {'DNA': 'AGTCC-TAAGGTCGCCAATGGGCA', 'protein': 'MKERBGWAQ--QGKKPWRF--EEW'}
# User visits the formalign.eu site.
self.browser.get(self.url + '/')
# She clicks the DNA button
seq_type_button = self.browser.find_element_by_css_selector(seq_type_button_dict[kwargs['seq_type']])
seq_type_button.click()
# She is so excited that she inadvertently submits the empty input
self.browser.find_element_by_id('submit-align').click()
# Wait for Firefox
time.sleep(self.wait)
self.assertEqual('Formalign.eu Home', self.browser.title, self.browser.title)
error = self.browser.find_element_by_css_selector('.errorlist').find_element_by_tag_name('li')
self.assertEqual(
EMPTY_ERROR,
error.text
)
# She decides to try it out so she pastes in an alignment and submits
alignment_input = self.browser.find_element_by_css_selector('textarea#id_align_input')
alignment_string = file_to_string(kwargs['seq_type'] + '_invalid_fasta.fasta')
alignment_input.send_keys(alignment_string)
self.browser.find_element_by_id('submit-align').click()
# Wait for Firefox
time.sleep(self.wait)
# unfortunately her FASTA format is invalid so she gets redirected to the submission form where she sees an
# error message telling her that her FASTA format is invalid
self.assertEqual(self.browser.title, 'Formalign.eu Home', self.browser.title)
error = self.browser.find_element_by_css_selector('.errorlist').find_element_by_tag_name('li')
self.assertEqual(
FORMAT_ERROR,
error.text
)
# she corrects her alignment and resubmits
alignment_string = file_to_string(kwargs['seq_type'] + '_invalid_characters.fasta')
alignment_input = self.browser.find_element_by_css_selector('textarea#id_align_input')
alignment_input.clear()
alignment_input.send_keys(alignment_string)
self.browser.find_element_by_id('submit-align').click()
# Wait for Firefox
time.sleep(self.wait)
# unfortunately now her sequences contain invalid characters so she gets redirected to the submission form
# again where she sees an error message telling her that her sequences contain invalid characters
self.assertEqual(self.browser.title, 'Formalign.eu Home', self.browser.title)
error = self.browser.find_element_by_css_selector('.errorlist').find_element_by_tag_name('li')
self.assertEqual(
CHARACTER_ERROR + 'sequence1',
error.text
)
# she corrects her alignment again and resubmits
alignment_string = file_to_string(kwargs['seq_type'] + '_too_few_sequences.fasta')
alignment_input = self.browser.find_element_by_css_selector('textarea#id_align_input')
alignment_input.clear()
alignment_input.send_keys(alignment_string)
self.browser.find_element_by_id('submit-align').click()
# Wait for Firefox
time.sleep(self.wait)
# unfortunately this time she accidentally erased one sequence and is left with only one sequence so she gets
# redirected to the submission form again where she sees an error message telling her that her alignment is not
# an alignment since it contains only one sequence
self.assertEqual('Formalign.eu Home', self.browser.title, self.browser.title)
error = self.browser.find_element_by_css_selector('.errorlist').find_element_by_tag_name('li')
self.assertEqual(
LESS_THAN_TWO_SEQS_ERROR,
error.text,
)
# she adds the missing sequence and resubmits
alignment_string = file_to_string(kwargs['seq_type'] + '_invalid_alignment.fasta')
alignment_input = self.browser.find_element_by_css_selector('textarea#id_align_input')
alignment_input.clear()
alignment_input.send_keys(alignment_string)
self.browser.find_element_by_id('submit-align').click()
# Wait for Firefox
time.sleep(self.wait)
# it must be starting to be a bit late since she added some residues to her first sequence so it is longer than
# the second now so she gets redirected to the submission form again where she sees an error message telling her
# that her alignment is not an alignment since the sequences do not all have the same length
self.assertEqual(self.browser.title, 'Formalign.eu Home', self.browser.title)
error = self.browser.find_element_by_css_selector('.errorlist').find_element_by_tag_name('li')
self.assertEqual(
ALIGNMENT_ERROR,
error.text,
)
# She tries one final time and threatens to throw her laptop out of the window if she gets another
# error message
alignment_string = file_to_string(kwargs['seq_type'] + '.fasta')
alignment_input = self.browser.find_element_by_css_selector('textarea#id_align_input')
alignment_input.clear()
alignment_input.send_keys(alignment_string)
self.browser.find_element_by_id('submit-align').click()
# Wait for Firefox
time.sleep(self.wait * 5)
# She got it right this time and is redirected to a page showing the submitted sequences from her alignment
self.assertEqual(self.browser.title, 'Formalign.eu Sequence Display', self.browser.title)
first_seq_info = self.browser.find_elements_by_css_selector('.query_seq_meta')[0]
self.assertEqual(
'sequence1:',
first_seq_info.text
)
first_seq_content = self.browser.find_elements_by_css_selector('.query_seq_display')[0]
self.assertIsNotNone(first_seq_content)
self.assertEqual(first_seq_content.text, test_seq[kwargs['seq_type']])
def test_basic_user_experience(self):
"""
Tests basic user interaction with formalign.eu site
"""
# Lambda user is a biologist who has to make a nice figure containing a multiple alignment for a presentation.
# She visits the formalign.eu site.
self.browser.get(self.url + "/")
# User sees she's on the right page because she can see the name of the site in the heading.
self.assertEqual(self.browser.title, "Formalign.eu Home", self.browser.title)
brand_element = self.browser.find_element_by_css_selector(".navbar-brand")
self.assertEqual("Formalign.eu", brand_element.text)
# She sees a form that says 'Paste in your alignment in FASTA format:'
alignment_input = self.browser.find_element_by_css_selector("textarea#id_align_input")
self.assertIsNotNone(self.browser.find_element_by_css_selector('label[for="id_align_input"]'))
self.assertEqual(
"Alignment (FASTA, clustalw, stockholm or phylip)", alignment_input.get_attribute("placeholder")
)
# She sees two radio buttons for DNA and protein
dna_button = self.browser.find_element_by_css_selector("input#id_seq_type_1")
self.assertIsNotNone(dna_button)
protein_button = self.browser.find_element_by_css_selector("input#id_seq_type_0")
self.assertIsNotNone(protein_button)
# She sees that the DNA button is selected by default
self.assertEqual(dna_button.is_selected(), True)
# She clicks the Protein radio button and sees that it gets selected and the DNA button gets unselected
protein_button.click()
# Wait for Firefox
time.sleep(self.sleep)
self.assertEqual(protein_button.is_selected(), True)
self.assertEqual(dna_button.is_selected(), False)
# She pastes in a protein alignment to see what happens
alignment_string = file_to_string("spa_protein_alignment.fasta")
pyperclip.copy(alignment_string)
alignment_input = self.browser.find_element_by_css_selector("textarea#id_align_input")
alignment_input.send_keys(Keys.CONTROL, "v")
self.browser.find_element_by_id("submit-align").click()
# Wait for Firefox
time.sleep(self.sleep * 5)
# She is redirected to a page showing the submitted sequences from her alignment and a simple consensus sequence
self.assertEqual(self.browser.title, "Formalign.eu Sequence Display", self.browser.title)
seq_content = self.browser.find_elements_by_css_selector(".query_seq_display")
self.assertIsNotNone(seq_content)
for f in seq_content:
self.assertTrue(len(f.text) <= 80)
first_seq_info = self.browser.find_elements_by_css_selector(".query_seq_meta")[0]
self.assertEqual(
"NP_175717 NP_175717.1 SPA1-related 4 protein [Arabidopsis thaliana].:",
first_seq_info.text,
first_seq_info.text,
)
first_seq_content = self.browser.find_elements_by_css_selector(".query_seq_display")[0]
self.assertIsNotNone(first_seq_content)
self.assertEqual(first_seq_content.text, "-" * 80)
consensus_seq = self.browser.find_elements_by_xpath('//div[@class="query_seq bg-color-body"]')[
-1
].find_elements_by_xpath('./p[@class="query_seq_display"]')[0]
self.assertIsNotNone(consensus_seq)
cons_seq = file_to_string("consensus.txt")
self.assertEqual(consensus_seq.text, cons_seq[:80])
consensus_meta = self.browser.find_elements_by_xpath('//h3[@class="query_seq_meta bg-color-body"]')[-1]
self.assertEqual(consensus_meta.text, "consensus 70%:")
# She is happy with the result, sees a "Render" button and clicks it.
render_button = self.browser.find_element_by_css_selector("button#render-align")
self.assertIsNotNone(render_button)
render_button.click()
# Wait for Firefox
time.sleep(self.sleep * 10)
# She is redirected to the alignment display page
self.assertEqual("Formalign.eu Alignment Display", self.browser.title, self.browser.title)
# She sees the alignment displayed with 80 characters per line in blocks of 10 with sequence ids
s0 = self.browser.find_elements_by_xpath('//tr[@class="al_ln"]')[10].find_elements_by_xpath(
'./td[@class="residue S0"]'
)
s1 = self.browser.find_elements_by_xpath('//tr[@class="al_ln"]')[10].find_elements_by_xpath(
'./td[@class="residue S1"]'
)
self.assertEqual(len(s0) + len(s1), 80)
sep = self.browser.find_elements_by_xpath('//tr[@class="al_ln"]')[10].find_elements_by_xpath(
'./td[@class="block_sep"]'
)
self.assertEqual(len(sep), 8)
# She is quite happy with the result and decides to try with another alignment so she navigates back to the
# home page
home_button = self.browser.find_element_by_css_selector(".navbar-brand")
home_button.click()
# Wait for Firefox
time.sleep(self.sleep * 2)
self.assertEqual("Formalign.eu Home", self.browser.title, self.browser.title)
# She wants to upload a protein stockholm alignment this time from a file
# She clicks the Protein radio button and sees that it gets selected and the DNA button gets unselected
protein_button = self.browser.find_element_by_css_selector("input#id_seq_type_0")
protein_button.click()
self.assertEqual(protein_button.is_selected(), True)
def test_index(self):
"""
Tests index page
"""
# Lambda user is a biologist who has to make a nice figure containing a multiple alignment for a presentation.
# She visits the formalign.eu site.
r = self.client.get(self.url)
csrftoken = self.client.cookies["csrftoken"]
index = html.parse(StringIO(r.text)).getroot()
title = index.cssselect('title[id="head-title"]')
brand = index.cssselect('a[class="navbar-brand"]')
align_input = index.cssselect('textarea[id="id_align_input"]')
prot_button = index.cssselect('input[id="id_seq_type_0"]')
prot_button_label = index.cssselect('label[for="id_seq_type_0"]')
dna_button = index.cssselect('input[id="id_seq_type_1"]')
# page displays no error message
self.assertEqual(r.status_code, 200, r.status_code)
# User sees she's on the right page because she can see the name of the site in the title and the brand.
self.assertEqual("Formalign.eu Home", title[0].text_content(), title[0].text_content())
self.assertEqual(self.url + "/", r.url, r.url)
self.assertEqual("Formalign.eu", brand[0].text_content(), brand[0].text_content())
# She sees a form that says 'Paste in your alignment'
self.assertEqual(
"Paste in your alignment:(FASTA, clustalw, stockholm or phylip)",
align_input[0].label.text_content(),
align_input[0].label.text_content(),
)
# There's a textarea with a placeholder saying 'Alignment'
self.assertEqual(
"Alignment (FASTA, clustalw, stockholm or phylip)",
align_input[0].attrib.get("placeholder"),
align_input[0].attrib.get("placeholder"),
)
# She sees two radio buttons for DNA and protein
self.assertEqual(
"Input sequence type:", prot_button[0].label.text_content(), prot_button[0].label.text_content()
)
self.assertEqual(" Protein", prot_button_label[1].text_content(), prot_button_label[1].text_content())
self.assertEqual(" DNA", dna_button[0].label.text_content(), dna_button[0].label.text_content())
# She sees that the DNA button is selected by default
self.assertTrue(prot_button[0].checkable, "Protein button is not checkable")
self.assertFalse(prot_button[0].checked, "Protein button was checked by default")
self.assertTrue(dna_button[0].checkable, "DNA button is not checkable")
self.assertTrue(dna_button[0].checked, "DNA button was not checked by default")
# She checks the protein button and pastes in an alignment
alignment_string = file_to_string("spa_protein_alignment.fasta")
self.client.headers.update({"referer": self.url})
r = self.client.post(
self.url, data={"csrfmiddlewaretoken": csrftoken, "seq_type": "Protein", "align_input": alignment_string}
)
self.assertEqual(r.status_code, 200, r.status_code)
display = html.parse(StringIO(r.text)).getroot()
title = display.cssselect('title[id="head-title"]')
# She is redirected to the sequence display page
self.assertEqual("Formalign.eu Sequence Display", title[0].text_content(), title[0].text_content())
self.assertEqual(
"%s/query-sequences" % self.url, "/".join(r.url.split("/")[:-2]), "/".join(r.url.split("/")[:-2])
)
def test_alignment_display(self):
"""
Tests alignment display page
"""
# User visits home page, submits a protein alignment and renders it
self.client.get(self.url)
csrftoken = self.client.cookies["csrftoken"]
alignment_string = file_to_string("spa_protein_alignment.fasta")
self.client.headers.update({"referer": self.url})
r = self.client.post(
self.url, data={"csrfmiddlewaretoken": csrftoken, "seq_type": "Protein", "align_input": alignment_string}
)
render_form = html.parse(StringIO(r.text)).getroot().cssselect('form[id="render"]')
r = self.client.get(self.url + render_form[0].attrib.get("action"))
# She is redirected to the render page
self.assertEqual(r.status_code, 200, r.status_code)
align = html.parse(StringIO(r.text)).getroot()
title = align.cssselect('title[id="head-title"]')
self.assertEqual("Formalign.eu Alignment Display", title[0].text_content(), title[0].text_content())
self.assertEqual(
"%s/align-display" % self.url, "/".join(r.url.split("/")[:-2]), "/".join(r.url.split("/")[:-2])
)
# She sees the alignment displayed with 80 characters per line in blocks of 10 with sequence ids
seqs_meta = file_to_string("spa_protein_alignment_meta.txt").splitlines()
tables = align.find_class("align_table")
for nr, t in enumerate(tables):
lines = t.find_class("al_ln")
for i, l in enumerate(lines):
self.assertEqual("seq_id", l[0].attrib.get("class"), l[0].attrib.get("class"))
self.assertEqual(seqs_meta[i], l[0].text_content(), l[0].text_content())
self.assertTrue(len(l[1:]) <= 89, len(l[1:]))
self.assertEqual("display_artifact", l[-1].attrib.get("class"))
if len(l[1:]) >= 12:
for j in range(1, len(l[1:]) % 10):
self.assertEqual(
"block_sep",
l[j * 11].attrib.get("class"),
"line number: %s, line length: %s, column: %s" % (i, len(l), format(j * 11)),
)
for k in range(j * 11 - 10, j * 11):
self.assertTrue(
l[k].attrib.get("class") == "residue S0" or l[k].attrib.get("class") == "residue S1",
"class: %s, table: %s, line: %s, column: %s" % (l[k].attrib.get("class"), nr, i, k),
)
else:
for j in range(1, len(l)):
self.assertTrue(
l[j].attrib.get("class") == "residue S0" or l[j].attrib.get("class") == "residue S1",
l[j].attrib.get("class"),
)
# She is quite happy with the result and decides to navigate back to the home page
home_button = align.cssselect('a[class="navbar-brand"]')
self.assertEqual("Formalign.eu", home_button[0].text_content(), home_button[0].text_content())
r = self.client.get(self.url + home_button[0].attrib.get("href"))
self.assertEqual(r.status_code, 200, r.status_code)
home = html.parse(StringIO(r.text)).getroot()
title = home.cssselect('title[id="head-title"]')
# User sees she's that she's back on the home page she can see the name of the site in the title and the brand.
self.assertEqual("Formalign.eu Home", title[0].text_content(), title[0].text_content())
self.assertEqual(self.url + "/", r.url, r.url)
