def test_file_missing_columns(self):
tc.formfile(
2, 'domains_emails',
os.path.join(os.path.dirname(__file__),
'data/domain_2016-09-16_missing_column_id.csv'))
tc.submit()
tc.find('Missing column "Id" on the row 2.')
def test_image_processing_library_error(self):
"""
If the image processing library errors while preparing a photo, report a
helpful message to the user and log the error. The photo is not added
to the user's profile.
"""
# Get a copy of the error log.
string_log = StringIO.StringIO()
logger = logging.getLogger()
my_log = logging.StreamHandler(string_log)
logger.addHandler(my_log)
logger.setLevel(logging.ERROR)
self.login_with_twill()
tc.go(make_twill_url('http://openhatch.org/people/paulproteus/'))
tc.follow('photo')
# This is a special image from issue166 that passes Django's image
# validation tests but causes an exception during zlib decompression.
tc.formfile('edit_photo', 'photo', photo('static/images/corrupted.png'))
tc.submit()
tc.code(200)
self.assert_("Something went wrong while preparing this" in tc.show())
p = Person.objects.get(user__username='******')
self.assertFalse(p.photo.name)
# an error message was logged during photo processing.
self.assert_("zlib.error" in string_log.getvalue())
logger.removeHandler(my_log)
def upload(self, input):
self.get("/tool_runner/index?tool_id=upload1")
tc.fv("1", "file_type", "bed")
tc.fv("1", "dbkey", input.get('dbkey', '?'))
tc.formfile("1", "file_data", input['file_path'])
tc.submit("runtool_btn")
tc.code(200)
def test_file_with_invalid_id(self):
tc.formfile(
2, 'domains_emails',
os.path.join(os.path.dirname(__file__),
'data/domain_2016-09-16_invalid_id.csv'))
tc.submit()
tc.find(
'Invalid value in column Id: "asdf9". It must be a whole number.')
def upload_file(self, fname, ftype='auto', dbkey='hg17'):
"""Uploads a file"""
fname = self.get_fname(fname)
tc.go("./tool_runner/index?tool_id=upload1")
tc.fv("1","file_type", ftype)
tc.fv("1","dbkey", dbkey)
tc.formfile("1","file_data", fname)
tc.submit("runtool_btn")
self.home()
def test_set_avatar(self):
self.login_with_twill()
for image in (photo("static/sample-photo.png"), photo("static/sample-photo.jpg")):
url = "http://openhatch.org/people/1/"
tc.go(make_twill_url(url))
tc.follow("photo")
tc.formfile("edit_photo", "photo", image)
tc.submit()
# Now check that the photo == what we uploaded
p = Person.objects.get(user__username="******")
self.assert_(p.photo.read() == open(image).read())
def test_set_avatar_too_wide(self):
self.login_with_twill()
for image in [photo("static/images/too-wide.jpg"), photo("static/images/too-wide.png")]:
url = "http://openhatch.org/people/1/"
tc.go(make_twill_url(url))
tc.follow("photo")
tc.formfile("edit_photo", "photo", image)
tc.submit()
# Now check that the photo is 200px wide
p = Person.objects.get(user__username="******")
image_as_stored = mysite.base.depends.Image.open(p.photo.file)
w, h = image_as_stored.size
self.assertEqual(w, 260)
def test_set_avatar(self):
self.login_with_twill()
for image in (photo('static/sample-photo.png'),
photo('static/sample-photo.jpg')):
url = 'http://openhatch.org/people/paulproteus/'
tc.go(make_twill_url(url))
tc.follow('photo')
tc.formfile('edit_photo', 'photo', image)
tc.submit()
# Now check that the photo == what we uploaded
p = Person.objects.get(user__username='******')
self.assert_(p.photo.read() ==
open(image).read())
def test_set_avatar_too_wide(self):
self.login_with_twill()
for image in [photo('static/images/too-wide.jpg'),
photo('static/images/too-wide.png')]:
url = 'http://openhatch.org/people/paulproteus/'
tc.go(make_twill_url(url))
tc.follow('photo')
tc.formfile('edit_photo', 'photo', image)
tc.submit()
# Now check that the photo is 200px wide
p = Person.objects.get(user__username='******')
image_as_stored = Image.open(p.photo.file)
w, h = image_as_stored.size
self.assertEqual(w, 200)
def test_file_unicode_in_email(self):
self.notif_mock.set_domain_outzone_unguarded_warning_emails.side_effect = \
Registry.Notification.DOMAIN_EMAIL_VALIDATION_ERROR(
[Registry.Notification.DomainEmail(domain_id=4, email='[email protected]\xc2\xa0')]
)
tc.formfile(
2, 'domains_emails',
os.path.join(os.path.dirname(__file__),
'data/domain_2017-02-01_unicode_in_email.csv'))
tc.submit()
tc.find(
'The file contains these invalid emails: [email protected]\xc2\xa0'
.decode('utf-8'))
def test_file_ok(self):
tc.formfile(
2, 'domains_emails',
os.path.join(os.path.dirname(__file__),
'data/domain_2016-09-16_OK.csv'))
tc.submit()
assert_equal(self.notif_mock.mock_calls, [
call.set_domain_outzone_unguarded_warning_emails([
Registry.Notification.DomainEmail(domain_id=4,
email='*****@*****.**'),
Registry.Notification.DomainEmail(domain_id=9,
email='*****@*****.**'),
Registry.Notification.DomainEmail(domain_id=9,
email='*****@*****.**')
])
])
tc.find(
r'Emails have been successfully saved. \(2 domains, 3 emails\)')
def annotate(params, proteins, \
url="http://signalfind.org/tatfind.html", force=False):
"""
Interfaces with the TatFind web service at (http://signalfind.org/tatfind.html)
to predict if protein sequences contain Twin-Arginine Translocation (Tat)
signal peptides.
"""
# set the user-agent so web services can block us if they want ... :/
python_version = sys.version.split()[0]
agent("Python-urllib/%s (twill; inmembrane)" % python_version)
outfn = 'tatfind.out'
log_stderr("# TatFind(web) %s > %s" % (params['fasta'], outfn))
if not force and os.path.isfile(outfn):
log_stderr("# -> skipped: %s already exists" % outfn)
fh = open(outfn, 'r')
proteins = parse_tatfind_output(fh, proteins)
fh.close()
return proteins
# dump extraneous output into this blackhole so we don't see it
if not __DEBUG__: twill.set_output(StringIO.StringIO())
go(url)
if __DEBUG__: showforms()
formfile("1", "seqFile", params["fasta"])
submit()
if __DEBUG__: show()
tatfind_output = show()
if __DEBUG__: log_stderr(tatfind_output)
# write raw TatFind output to a file
fh = open(outfn, 'w')
fh.write(tatfind_output)
fh.close()
proteins = parse_tatfind_output(tatfind_output.split("\n"), proteins)
return proteins
def test_set_avatar(self):
self.login_with_twill()
for image in [photo('static/sample-photo.png'),
photo('static/sample-photo.jpg')]:
url = 'http://openhatch.org/people/paulproteus/'
tc.go(make_twill_url(url))
tc.follow('photo')
tc.formfile('edit_photo', 'photo', image)
tc.submit()
# Now check that the photo == what we uploaded
p = Person.objects.get(user__username='******')
self.assert_(p.photo.read() ==
open(image).read())
response = self.login_with_client().get(reverse(mysite.account.views.edit_photo))
self.assertEqual( response.context[0]['photo_url'], p.photo.url,
"Test that once you've uploaded a photo via the photo editor, "
"the template's photo_url variable is correct.")
self.assert_(p.photo_thumbnail)
thumbnail_as_stored = mysite.base.depends.Image.open(p.photo_thumbnail.file)
w, h = thumbnail_as_stored.size
self.assertEqual(w, 40)
def test_invalid_photo(self):
"""
If the uploaded image is detected as being invalid, report a helpful
message to the user. The photo is not added to the user's profile.
"""
bad_image = tempfile.NamedTemporaryFile(delete=False)
self.login_with_twill()
try:
bad_image.write("garbage")
bad_image.close()
tc.go(make_twill_url("http://openhatch.org/people/1/"))
tc.follow("photo")
tc.formfile("edit_photo", "photo", bad_image.name)
tc.submit()
tc.code(200)
self.assert_("The file you uploaded was either not an image or a " "corrupted image" in tc.show())
p = Person.objects.get(user__username="******")
self.assertFalse(p.photo.name)
finally:
os.unlink(bad_image.name)
def upload(self, file):
self.get("/tool_runner/index?tool_id=upload1")
tc.fv("1","file_type", "bed")
tc.formfile("1","file_data", file)
tc.submit("runtool_btn")
tc.code(200)
def annotate(params, proteins, \
url="http://rbf.bioinfo.tw/"+
"~sachen/OMPpredict/"+
"TMBETADISC-RBF-Content.html", force=False):
"""
Interfaces with the TatFind web service at
(http://rbf.bioinfo.tw/~sachen/OMPpredict/TMBETADISC-RBF.php)
to predict if protein sequence is likely to be an outer membrane beta-barrel.
Note that the default URL we use it different to the regular form used
by web browsers, since we need to bypass some AJAX fun.
"""
# TODO: automatically split large sets into multiple jobs
# since TMBETADISC seems to not like more than take
# ~5000 seqs at a time
if len(proteins) >= 5000:
log_stderr("# ERROR: TMBETADISC-RBF(web): tends to fail with > ~5000 sequences.")
return
# set the user-agent so web services can block us if they want ... :/
python_version = sys.version.split()[0]
agent("Python-urllib/%s (twill; inmembrane)" % python_version)
outfn = 'tmbetadisc-rbf.out'
log_stderr("# TMBETADISC-RBF(web) %s > %s" % (params['fasta'], outfn))
if not force and os.path.isfile(outfn):
log_stderr("# -> skipped: %s already exists" % outfn)
fh = open(outfn, 'r')
proteins = parse_tmbetadisc_output(fh.read(), proteins)
fh.close()
return proteins
# dump extraneous output into this blackhole so we don't see it
if not __DEBUG__: twill.set_output(StringIO.StringIO())
go(url)
if __DEBUG__: showforms()
formfile("1", "userfile", params["fasta"])
fv("1", "format", "file")
# set the user defined method
method_map = {"aa":"Amino Acid Composition",
"dp":"Depipetide Composition",
"aadp":"Amino Acid & Depipetide Composition",
"pssm":"PSSM"}
if dict_get(params, 'tmbetadisc_rbf_method'):
try:
method = method_map[params['tmbetadisc_rbf_method']]
except KeyError:
log_stderr("# ERROR: Invalid setting from tmbetadisc_rbf_method. \
Must be set to aa, dp, aadp or pssm.")
sys.exit()
#fv("1", "select", "Amino Acid Composition")
#fv("1", "select", "Depipetide Composition")
#fv("1", "select", "Amino Acid & Depipetide Composition")
#fv("1", "select", "PSSM")
fv("1", "select", method)
submit()
waiting_page = show()
if __DEBUG__: log_stderr(waiting_page)
for l in waiting_page.split('\n'):
if l.find("TMBETADISC-RBF-action.php?UniqueName=") != -1:
result_url = l.split("'")[1]
time.sleep(5)
go(result_url)
output = show()
if __DEBUG__: log_stderr(output)
# write raw output to a file
fh = open(outfn, 'w')
fh.write(output)
fh.close()
proteins = parse_tmbetadisc_output(output, proteins)
return proteins
def test():
url = twilltestlib.get_url()
# test empty page get_title
namespaces.new_local_dict()
twill.commands.reset_browser()
browser = twill.get_browser()
try:
browser.get_title()
assert 0, "should never get here"
except BrowserStateError:
pass
### now test a few special cases
commands.go(url)
commands.go('/login')
commands.showforms()
# test no matching forms
try:
commands.fv('2', 'submit', '1')
assert 0
except TwillAssertionError:
pass
# test regexp match
commands.fv('1', '.*you', '1')
# test ambiguous match to value
commands.go('/testform')
commands.fv('1', 'selecttest', 'val')
commands.fv('1', 'selecttest', 'value1')
commands.fv('1', 'selecttest', 'selvalue1')
commands.formclear('1')
try:
commands.fv('1', 'selecttest', 'value')
assert 0
except ClientForm.ItemNotFoundError:
pass
# test ambiguous match to name
commands.go('/testform')
try:
commands.fv('1', 'item_', 'value')
assert 0
except Exception:
pass
try:
commands.formfile('1', 'selecttest', 'null')
assert 0
except Exception:
pass
commands.go('http://www.google.com/')
browser.get_title()
# test the twill script.
twilltestlib.execute_twill_script('test-form.twill', initial_url=url)
def test_empty_file_uploaded(self):
tc.formfile(2, 'domains_emails',
os.path.join(os.path.dirname(__file__), 'data/empty_file'))
tc.submit()
tc.find('Wrong file format.')
def annotate(params, proteins, \
url="http://services.cbu.uib.no/tools/bomp/", force=False):
"""
Uses the BOMP web service (http://services.cbu.uib.no/tools/bomp/) to
predict if proteins are outer membrane beta-barrels.
"""
# set the user-agent so web services can block us if they want ... :/
python_version = sys.version.split()[0]
agent("Python-urllib/%s (twill; inmembrane/%s)" %
(python_version, inmembrane.__version__))
bomp_out = 'bomp.out'
log_stderr("# BOMP(web) %s > %s" % (params['fasta'], bomp_out))
if not force and os.path.isfile(bomp_out):
log_stderr("# -> skipped: %s already exists" % bomp_out)
bomp_categories = {}
fh = open(bomp_out, 'r')
for l in fh:
words = l.split()
bomp_category = int(words[-1:][0])
seqid = parse_fasta_header(l)[0]
proteins[seqid]['bomp'] = bomp_category
bomp_categories[seqid] = bomp_category
fh.close()
return bomp_categories
# dump extraneous output into this blackhole so we don't see it
if not __DEBUG__: twill.set_output(StringIO.StringIO())
go(url)
if __DEBUG__: showforms()
formfile("1", "queryfile", params["fasta"])
submit()
if __DEBUG__: show()
# extract the job id from the page
links = showlinks()
job_id = None
for l in links:
if l.url.find("viewOutput") != -1:
# grab job id from "viewOutput?id=16745338"
job_id = int(l.url.split("=")[1])
if __DEBUG__: log_stderr("BOMP job id: %d" % job_id)
if not job_id:
# something went wrong
log_stderr("# BOMP error: Can't find job id")
return
# parse the HTML table and extract categories
go("viewOutput?id=%i" % (job_id))
polltime = 10
log_stderr("# Waiting for BOMP to finish .")
while True:
try:
find("Not finished")
log_stderr(".")
except:
# Finished ! Pull down the result page.
log_stderr(". done!\n")
go("viewOutput?id=%i" % (job_id))
if __DEBUG__: log_stderr(show())
break
# Not finished. We keep polling for a time until
# we give up
time.sleep(polltime)
polltime = polltime * 2
if polltime >= 7200: # 2 hours
log_stderr("# BOMP error: Taking too long.")
return
go("viewOutput?id=%i" % (job_id))
if __DEBUG__: log_stderr(show())
bomp_html = show()
if __DEBUG__: log_stderr(bomp_html)
# Results are in the only <table> on this page, formatted like:
# <tr><th>gi|107836852|gb|ABF84721.1<th>5</tr>
soup = BeautifulSoup(bomp_html)
bomp_categories = {} # dictionary of {name, category} pairs
for tr in soup.findAll('tr')[1:]:
n, c = tr.findAll('th')
name = parse_fasta_header(n.text.strip())[0]
category = int(c.text)
bomp_categories[name] = category
# write BOMP results to a tab delimited file
fh = open(bomp_out, 'w')
for k, v in bomp_categories.iteritems():
fh.write("%s\t%i\n" % (k, v))
fh.close()
if __DEBUG__: log_stderr(str(bomp_categories))
# label proteins with bomp classification (int) or False
for name in proteins:
if "bomp" not in proteins[name]:
if name in bomp_categories:
category = int(bomp_categories[name])
proteins[name]['bomp'] = category
else:
proteins[name]['bomp'] = False
if __DEBUG__: log_stderr(str(proteins))
return bomp_categories
"""
def upload_list(browser, pagename, uploads):
# get the file sizes for later comparison.
filesizes = []
for fn in uploads:
filesizes.append(os.stat(fn)[stat.ST_SIZE])
filesizes.reverse() # because they get listed newest first.
# Upload copy #1.
t.go(host + "index.php/Special:Upload")
t.formfile("1", "wpUploadFile", uploads[0])
t.fv("1", "wpDestFile", pagename)
t.fv("1", "wpUploadDescription", "Uploading %s" % pagename)
t.submit("wpUpload")
# Verify that we succeeded.
t.find("File:%s" % pagename)
for fn in uploads[1:]:
# propose that we upload a replacement
t.go(host + "index.php?title=Special:Upload&wpDestFile=%s&wpForReUpload=1" % pagename)
t.formfile("1", "wpUploadFile", fn)
t.fv("1", "wpUploadDescription", "Uploading %s as %s" % (fn, pagename))
t.submit("wpUpload")
# get the URLs for the thumbnails
urls = []
for url in re.finditer(
r'<td><a href="([^"]*?)"><img alt="Thumbnail for version .*?" src="(.*?)"', browser.get_html()
):
urls.append(url.group(1))
urls.append(url.group(2))
print filesizes
for i, url in enumerate(urls):
t.go(url)
if i % 2 == 0 and len(browser.get_html()) != filesizes[i / 2]:
print i, len(browser.get_html()), filesizes[i / 2]
t.find("Files differ in size")
t.code("200")
t.back()
# delete all versions
t.go(host + "index.php?title=File:%s&action=delete" % pagename)
# after we get the confirmation page, commit to the action.
t.fv("1", "wpReason", "Test Deleting...")
t.submit("mw-filedelete-submit")
# make sure that we can't visit their URLs.
for i, url in enumerate(urls):
t.go(url)
if 0 and i % 2 == 1 and i > 0 and browser.get_code() == 200:
# bug 30192: the archived file's thumbnail doesn't get deleted.
print "special-casing the last URL"
continue
t.code("404")
# restore the current and archived version.
t.go(host + "index.php/Special:Undelete/File:%s" % pagename)
t.fv("1", "wpComment", "Test Restore")
t.submit("restore")
# visit the page to make sure that the thumbs get re-rendered properly.
# when we get the 404 handler working correctly, this won't be needed.
t.go(host + "index.php?title=File:%s" % pagename)
# make sure that they got restored correctly.
for i, url in enumerate(urls):
t.go(url)
if i % 2 == 0 and len(browser.get_html()) != filesizes[i / 2]:
t.find("Files differ in size")
t.code("200")
t.back()
if len(uploads) != 2:
return
match = re.search(r'"([^"]+?)" title="[^"]+?">revert', browser.get_html())
if not match:
t.find("revert")
t.go(match.group(1).replace("&", "&"))
def test_data_uploads(self):
# data upload test
name = 'Upload-test-name'
self.create_project(name)
tc.follow(name)
# find the project id
url = tc.follow('Edit')
pid = url.split("/")[-2]
tc.go("/data/upload/simple/%s/" % pid)
# search for then add Demo User to this project
tc.formfile("1", "File1", conf.testdata('short-data.bed') )
tc.formfile("1", "File2", conf.testdata('short-good-input.gtrack') )
tc.formfile("1", "File3", conf.testdata('readcounts.png') )
tc.submit()
# verify uploads
tc.find("short-data.bed")
tc.find("short-good-input.gtrack")
tc.find("readcounts.png")
# visit the dataset
tc.follow("short-good-input.gtrack")
tc.find("waiting")
# edit the dataset
tc.follow("Edit")
tc.fv("1", "name", "short-good-input.gtrack" )
tc.fv("1", "info","extra-info" )
tc.submit()
tc.find("extra-info")
# upload two results for it
tc.follow("Add results")
tc.formfile("1", "content", conf.testdata('short-data.bed') )
tc.formfile("1", "image", conf.testdata('readcounts.png') )
tc.submit()
tc.follow("short-data.bed")
tc.back()
# upload one image
tc.follow("Add results")
tc.formfile("1", "image", conf.testdata('shift.png') )
tc.submit()
tc.follow("shift.png")
tc.back()
# back to project view
tc.follow("Project view")
self.delete_project(name)
