class StudyTests(TestCase):
def setUp(self):
# create a clinical study
self.study = Study(
title="Can teeth bite?",
slug="can-teeth-bite",
date=datetime.now(),
)
def test_generic_attributes(self):
self.study.save()
# the item has no informative content
self.assertEqual(self.study.is_uninformative, True)
# no Entities in the database, so this can't be hosted_by anything
self.assertEqual(self.study.hosted_by, None)
# no Entities in the database, so default to settings's template
self.assertEqual(
self.study.get_template,
settings.CMS_TEMPLATES[0][0]
)
def test_link_to_more(self):
self.assertEqual(
self.study.auto_page_view_name,
"clinical-studies"
)
self.study.hosted_by = Entity(slug="slug")
self.assertEqual(
self.study.link_to_more(),
"/clinical-studies/slug/"
)
def setUp(self):
# create a clinical study
self.study = Study(
title="Can teeth bite?",
slug="can-teeth-bite",
date=datetime.now(),
)
def setUp(self):
self.item1 = Study(
title="newer",
in_lists=True,
published=True,
date=datetime.now(),
slug="item1"
)
self.item1.save()
self.item2 = Study(
title="older",
in_lists=True,
published=True,
date=datetime.now()-timedelta(days=200),
slug="item2"
)
self.item2.save()
self.item3 = Study(
title="unpublished",
in_lists=True,
published=False,
date=datetime.now(),
slug="item3"
)
self.item1.save()
self.itemlist = StudiesList(request=RequestFactory().get("/"))
def setUp(self):
home_page = create_page("School home page",
"null.html",
"en",
published=True)
self.school = Entity(name="School of Medicine",
slug="medicine",
auto_news_page=True,
website=home_page)
self.item1 = Study(title="newer",
in_lists=True,
published=True,
date=datetime.now(),
slug="item1")
self.item1.save()
self.item2 = Study(title="older",
in_lists=True,
published=True,
date=datetime.now() - timedelta(days=200),
slug="item2")
self.item2.save()
self.item3 = Study(title="unpublished",
in_lists=True,
published=False,
date=datetime.now(),
slug="item3")
self.item1.save()
self.itemlist = StudiesList(request=RequestFactory().get("/"))
def setUp(self):
self.item1 = Study(title="newer", slug="item1")
self.adminuser = User.objects.create_user('arkestra',
'*****@*****.**',
'arkestra')
self.adminuser.is_staff = True
self.adminuser.save()
def new_study(request):
if request.method == 'POST':
sform = StudyForm(request.POST, instance=Study())
if sform.is_valid():
sform.save()
return HttpResponseRedirect('/viewer/new_study/')
else:
sform = StudyForm(instance=Study())
context = {'study_form': sform}
studies = Study.objects.all()
context['studies'] = studies
context.update(csrf(request))
return render_to_response('viewer/new_study.html',
context,
context_instance=RequestContext(request))
def aggregatable_study_properties():
"""
Same behaviour as /properties, but excludes fields that it doesn't make
sense to generate charts / aggregations from
"""
app.logger.info("/aggregatable_properties")
return jsonify({"properties": Study.valid_fields(True)})
def get_studies_json():
try:
update_lock.acquire()
global studies_text
return [Study(text).enriched_json() for text in studies_text]
finally:
update_lock.release()
def aggregatable_study_properties():
"""
Same behaviour as /properties, but excludes fields that it doesn't make
sense to generate charts / aggregations from
"""
app.logger.info("/aggregatable_properties")
return jsonify({"properties": Study.valid_fields(True)})
def setUp(self):
# create a clinical study
self.study = Study(
title="Can teeth bite?",
slug="can-teeth-bite",
date=datetime.now(),
)
def valid_study_properties():
"""
Return all the valid properties that can be used in filters and 'field'
query params in the REST API. Useful in combination with '/values' to allow
the user to dynamically choose fields to generate a visualization from.
"""
app.logger.info("/properties")
return jsonify({"properties": Study.valid_fields(False)})
def valid_study_properties():
"""
Return all the valid properties that can be used in filters and 'field'
query params in the REST API. Useful in combination with '/values' to allow
the user to dynamically choose fields to generate a visualization from.
"""
app.logger.info("/properties")
return jsonify({"properties": Study.valid_fields(False)})
def setUp(self):
home_page = create_page(
"School home page",
"null.html",
"en",
published=True
)
self.school = Entity(
name="School of Medicine",
slug="medicine",
auto_news_page=True,
website=home_page
)
self.item1 = Study(
title="newer",
in_lists=True,
published=True,
date=datetime.now(),
slug="item1"
)
self.item1.save()
self.item2 = Study(
title="older",
in_lists=True,
published=True,
date=datetime.now()-timedelta(days=200),
slug="item2"
)
self.item2.save()
self.item3 = Study(
title="unpublished",
in_lists=True,
published=False,
date=datetime.now(),
slug="item3"
)
self.item1.save()
self.itemlist = StudiesList(request=RequestFactory().get("/"))
class ClinicalEntityPagesTests(TestCase):
def setUp(self):
home_page = create_page(
"School home page",
"null.html",
"en",
published=True
)
self.school = Entity(
name="School of Medicine",
slug="medicine",
auto_news_page=True,
website=home_page
)
self.item1 = Study(
title="newer",
in_lists=True,
published=True,
date=datetime.now(),
slug="item1"
)
self.item1.save()
self.item2 = Study(
title="older",
in_lists=True,
published=True,
date=datetime.now()-timedelta(days=200),
slug="item2"
)
self.item2.save()
self.item3 = Study(
title="unpublished",
in_lists=True,
published=False,
date=datetime.now(),
slug="item3"
)
self.item1.save()
self.itemlist = StudiesList(request=RequestFactory().get("/"))
def test_main_url(self):
self.school.save()
response = self.client.get('/clinical-studies/')
self.assertEqual(response.status_code, 200)
self.assertItemsEqual(
response.context["lister"].lists[0].items,
[self.item1, self.item2]
)
def test_entity_url(self):
self.school.save()
response = self.client.get('/clinical-studies/medicine/')
self.assertEqual(response.status_code, 200)
def setUp(self):
self.item1 = Study(
title="newer",
slug="item1"
)
self.adminuser = User.objects.create_user(
'arkestra',
'*****@*****.**',
'arkestra'
)
self.adminuser.is_staff = True
self.adminuser.save()
def setUp(self):
self.item1 = Study(title="newer",
in_lists=True,
published=True,
date=datetime.now(),
slug="item1")
self.item1.save()
self.item2 = Study(title="older",
in_lists=True,
published=True,
date=datetime.now() - timedelta(days=200),
slug="item2")
self.item2.save()
self.item3 = Study(title="unpublished",
in_lists=True,
published=False,
date=datetime.now(),
slug="item3")
self.item1.save()
self.itemlist = StudiesList(request=RequestFactory().get("/"))
class StudyTests(TestCase):
def setUp(self):
# create a clinical study
self.study = Study(
title="Can teeth bite?",
slug="can-teeth-bite",
date=datetime.now(),
)
def test_generic_attributes(self):
self.study.save()
# the item has no informative content
self.assertEqual(self.study.is_uninformative, True)
# no Entities in the database, so this can't be hosted_by anything
self.assertEqual(self.study.hosted_by, None)
# no Entities in the database, so default to settings's template
self.assertEqual(self.study.get_template, settings.CMS_TEMPLATES[0][0])
def test_link_to_more(self):
self.assertEqual(self.study.auto_page_view_name, "clinical-studies")
self.study.hosted_by = Entity(slug="slug")
self.assertEqual(self.study.link_to_more(), "/clinical-studies/slug/")
def study():
ret = {}
try:
# count the no of lines
with open('uploads/study.csv') as f:
for i, l in enumerate(f):
pass
total_lines = i + 1
# getting the data from the csv file
csv_file = open('uploads/study.csv', 'r')
line = csv_file.readline()
cnt = 1
while cnt < total_lines:
line = csv_file.readline()
s = line.split(',')
id = s[0]
Paragraph_Number = id
Paragraph_Text = s[1]
Date_of_Upload = s[2]
Paragraph_Type = s[3]
Word_Count = s[4]
Status = s[5]
GCS_Output = s[6]
GCS_Acc = s[7]
GCS_Conf = s[8]
AH_Output = s[9]
AH_Acc = s[10]
AH_Conf = s[11]
Speaker = s[12]
study = Study(id, Paragraph_Number, Paragraph_Text, Date_of_Upload,
Paragraph_Type, Word_Count, Status, GCS_Output,
GCS_Acc, GCS_Conf, AH_Output, AH_Acc, AH_Conf,
Speaker)
db.session.add(study)
db.session.commit()
ret['success'] = True
ret['msg'] = 'Csv file is stored in the psql'
cnt += 1
except Exception as exp:
ret['success'] = False
ret['error'] = '%s' % exp
return jsonify(ret)
class StudyDetailTests(TestCase):
def setUp(self):
self.item1 = Study(
title="newer",
slug="item1"
)
self.adminuser = User.objects.create_user(
'arkestra',
'*****@*****.**',
'arkestra'
)
self.adminuser.is_staff = True
self.adminuser.save()
def test_unpublished_clinical_study_404(self):
self.item1.save()
response = self.client.get("/clinical-study/item1/")
self.assertEqual(response.status_code, 404)
def test_unpublished_clinical_study_200_for_admin(self):
self.item1.save()
# log in a staff user
self.client.login(username='******', password='******')
response = self.client.get('/clinical-study/item1/')
self.assertEqual(response.status_code, 200)
def test_published_clinical_study_200_for_everyone(self):
self.item1.published = True
self.item1.save()
# Check that the response is 200 OK.
response = self.client.get('/clinical-study/item1/')
self.assertEqual(response.status_code, 200)
def test_published_clinical_study_context(self):
self.item1.published = True
self.item1.save()
response = self.client.get('/clinical-study/item1/')
self.assertEqual(response.context['study'], self.item1)
class StudyListTests(TestCase):
def setUp(self):
self.item1 = Study(
title="newer",
in_lists=True,
published=True,
date=datetime.now(),
slug="item1"
)
self.item1.save()
self.item2 = Study(
title="older",
in_lists=True,
published=True,
date=datetime.now()-timedelta(days=200),
slug="item2"
)
self.item2.save()
self.item3 = Study(
title="unpublished",
in_lists=True,
published=False,
date=datetime.now(),
slug="item3"
)
self.item1.save()
self.itemlist = StudiesList(request=RequestFactory().get("/"))
def test_build(self):
self.itemlist.build()
self.assertItemsEqual(
self.itemlist.items,
[self.item1, self.item2]
)
def test_lister_has_list(self):
lister = StudiesLister(request=RequestFactory().get("/"))
self.assertIsInstance(lister.lists[0], StudiesList)
def test_list_has_correct_filter_fields(self):
self.assertItemsEqual(
self.itemlist.filter_set.fields,
["date", "status", "studytype"]
)
class ClinicalEntityPagesTests(TestCase):
def setUp(self):
home_page = create_page("School home page",
"null.html",
"en",
published=True)
self.school = Entity(name="School of Medicine",
slug="medicine",
auto_news_page=True,
website=home_page)
self.item1 = Study(title="newer",
in_lists=True,
published=True,
date=datetime.now(),
slug="item1")
self.item1.save()
self.item2 = Study(title="older",
in_lists=True,
published=True,
date=datetime.now() - timedelta(days=200),
slug="item2")
self.item2.save()
self.item3 = Study(title="unpublished",
in_lists=True,
published=False,
date=datetime.now(),
slug="item3")
self.item1.save()
self.itemlist = StudiesList(request=RequestFactory().get("/"))
def test_main_url(self):
self.school.save()
response = self.client.get('/clinical-studies/')
self.assertEqual(response.status_code, 200)
self.assertItemsEqual(response.context["lister"].lists[0].items,
[self.item1, self.item2])
def test_entity_url(self):
self.school.save()
response = self.client.get('/clinical-studies/medicine/')
self.assertEqual(response.status_code, 200)
class StudyDetailTests(TestCase):
def setUp(self):
self.item1 = Study(title="newer", slug="item1")
self.adminuser = User.objects.create_user('arkestra',
'*****@*****.**',
'arkestra')
self.adminuser.is_staff = True
self.adminuser.save()
def test_unpublished_clinical_study_404(self):
self.item1.save()
response = self.client.get("/clinical-study/item1/")
self.assertEqual(response.status_code, 404)
def test_unpublished_clinical_study_200_for_admin(self):
self.item1.save()
# log in a staff user
self.client.login(username='******', password='******')
response = self.client.get('/clinical-study/item1/')
self.assertEqual(response.status_code, 200)
def test_published_clinical_study_200_for_everyone(self):
self.item1.published = True
self.item1.save()
# Check that the response is 200 OK.
response = self.client.get('/clinical-study/item1/')
self.assertEqual(response.status_code, 200)
def test_published_clinical_study_context(self):
self.item1.published = True
self.item1.save()
response = self.client.get('/clinical-study/item1/')
self.assertEqual(response.context['study'], self.item1)
class StudyListTests(TestCase):
def setUp(self):
self.item1 = Study(title="newer",
in_lists=True,
published=True,
date=datetime.now(),
slug="item1")
self.item1.save()
self.item2 = Study(title="older",
in_lists=True,
published=True,
date=datetime.now() - timedelta(days=200),
slug="item2")
self.item2.save()
self.item3 = Study(title="unpublished",
in_lists=True,
published=False,
date=datetime.now(),
slug="item3")
self.item1.save()
self.itemlist = StudiesList(request=RequestFactory().get("/"))
def test_build(self):
self.itemlist.build()
self.assertItemsEqual(self.itemlist.items, [self.item1, self.item2])
def test_lister_has_list(self):
lister = StudiesLister(request=RequestFactory().get("/"))
self.assertIsInstance(lister.lists[0], StudiesList)
def test_list_has_correct_filter_fields(self):
self.assertItemsEqual(self.itemlist.filter_set.fields,
["date", "status", "studytype"])
def add_studies(request):
titles = request.POST['titles'].replace('\r', '').split('\n')
pmids = request.POST['pmids'].replace('\r', '').split('\n')
taxid = request.POST.get('species', None)
if taxid:
species = Species.objects.get(taxid=taxid)
comment = request.POST['comment'] or "Adding studies"
succieded = []
warned = []
failed = []
with reversion.create_revision():
#print "Titles", titles
#print "pmids", pmids
for title in titles:
if not title: continue
#print "Title:", title
#study, created = Study.objects.get_or_create(title=title)
study = Study(title=title)
study.save()
try:
print vars(study)
except UnicodeEncodeError as e:
print e
print study.reference_was_created
if not study.reference_was_created:#study.reference.authors:
warned.append(title)
messages.add_message(request, messages.WARNING, ugettext("Already in db: %s" % title))
created = False
else:
created = True
try:
study_confirm = Study.objects.get(title__icontains=title)
if study_confirm:
succieded.append(title)
print "Authors:", study.reference.authors
messages.add_message(request, messages.SUCCESS, ugettext("Succeeded: %s" % title))
else:
failed.append(title)
messages.add_message(request, messages.ERROR, ugettext("Failed: %s" % title))
if taxid:
study_confirm.species.add(species)
print("Adding species")
#study_confirm.save()
except Exception as e:
print e
failed.append(title)
messages.add_message(request, messages.ERROR, ugettext("Failed: %s" % title))
messages.add_message(request, messages.WARNING, ugettext("However added %s" % study.title))
if taxid:
print("Adding species")
try:
study.species.add(species)
except ValueError as e: #Exception Value: 'Study' instance needs to have a primary key value before a many-to-many relationship can be used.
messages.add_message(request, messages.ERROR, ugettext("Error: %s" % e))
log(request, study, comment)
for pmid in pmids:
if not pmid: continue
print "PMID:", pmid
study = Study(pmid=pmid)
study.save()
#print "views.add.studies for pmid in pmids:", vars(study)
if not study.reference_was_created:
warned.append(pmid)
messages.add_message(request, messages.WARNING, ugettext("Already in db: %s" % pmid))
created = False
else:
created = True
try:
study_confirm = Study.objects.get(pmid=pmid)
if study_confirm:
succieded.append(pmid)
messages.add_message(request, messages.SUCCESS, ugettext("Succeeded: %s" % pmid))
else:
failed.append(pmid)
messages.add_message(request, messages.ERROR, ugettext("Failed: %s" % pmid))
if taxid:
print("Adding species")
study_confirm.species.add(species)
except Exception as e:
print e
failed.append(pmid)
messages.add_message(request, messages.ERROR, ugettext("Failed: %s" % pmid))
messages.add_message(request, messages.WARNING, ugettext("However added %s" % study.pmid))
if taxid:
print("Adding species")
try:
study.species.add(species)
except ValueError as e:
messages.add_message(request, messages.ERROR, ugettext("Error: %s" % e))
log(request, study, comment)
if isinstance(request.user, AnonymousUser):
request.user = User.objects.get(username="******")
reversion.set_user(request.user)
reversion.set_comment(comment)
if succieded:
msg = "Successfully added the following %i studies: \n%s" % (len(succieded), "\n".join(succieded))
messages.add_message(request, messages.SUCCESS, ugettext(msg))
if warned:
msg = "Found already in db the following %i studies: \n%s" % (len(warned), "\n".join(warned))
messages.add_message(request, messages.WARNING, ugettext(msg))
if failed:
msg = "Failed to fetch information on the following %i studies: \n%s" % (len(failed), "\n".join(failed))
messages.add_message(request, messages.ERROR, ugettext(msg))
return HttpResponseRedirect('/lifespan/studies/')
def add_studies(request):
titles = request.POST['titles'].replace('\r', '').split('\n')
pmids = request.POST['pmids'].replace('\r', '').split('\n')
taxid = request.POST.get('species', None)
if taxid:
species = Species.objects.get(taxid=taxid)
comment = request.POST['comment'] or "Adding studies"
succieded = []
warned = []
failed = []
with reversion.create_revision():
#print "Titles", titles
#print "pmids", pmids
for title in titles:
if not title: continue
#print "Title:", title
#study, created = Study.objects.get_or_create(title=title)
study = Study(title=title)
study.save()
try:
print vars(study)
except UnicodeEncodeError as e:
print e
print study.reference_was_created
if not study.reference_was_created: #study.reference.authors:
warned.append(title)
messages.add_message(request, messages.WARNING,
ugettext("Already in db: %s" % title))
created = False
else:
created = True
try:
study_confirm = Study.objects.get(title__icontains=title)
if study_confirm:
succieded.append(title)
print "Authors:", study.reference.authors
messages.add_message(request, messages.SUCCESS,
ugettext("Succeeded: %s" % title))
else:
failed.append(title)
messages.add_message(request, messages.ERROR,
ugettext("Failed: %s" % title))
if taxid:
study_confirm.species.add(species)
print("Adding species")
#study_confirm.save()
except Exception as e:
print e
failed.append(title)
messages.add_message(request, messages.ERROR,
ugettext("Failed: %s" % title))
messages.add_message(
request, messages.WARNING,
ugettext("However added %s" % study.title))
if taxid:
print("Adding species")
try:
study.species.add(species)
except ValueError as e: #Exception Value: 'Study' instance needs to have a primary key value before a many-to-many relationship can be used.
messages.add_message(request, messages.ERROR,
ugettext("Error: %s" % e))
log(request, study, comment)
for pmid in pmids:
if not pmid: continue
print "PMID:", pmid
study = Study(pmid=pmid)
study.save()
#print "views.add.studies for pmid in pmids:", vars(study)
if not study.reference_was_created:
warned.append(pmid)
messages.add_message(request, messages.WARNING,
ugettext("Already in db: %s" % pmid))
created = False
else:
created = True
try:
study_confirm = Study.objects.get(pmid=pmid)
if study_confirm:
succieded.append(pmid)
messages.add_message(request, messages.SUCCESS,
ugettext("Succeeded: %s" % pmid))
else:
failed.append(pmid)
messages.add_message(request, messages.ERROR,
ugettext("Failed: %s" % pmid))
if taxid:
print("Adding species")
study_confirm.species.add(species)
except Exception as e:
print e
failed.append(pmid)
messages.add_message(request, messages.ERROR,
ugettext("Failed: %s" % pmid))
messages.add_message(request, messages.WARNING,
ugettext("However added %s" % study.pmid))
if taxid:
print("Adding species")
try:
study.species.add(species)
except ValueError as e:
messages.add_message(request, messages.ERROR,
ugettext("Error: %s" % e))
log(request, study, comment)
if isinstance(request.user, AnonymousUser):
request.user = User.objects.get(username="******")
reversion.set_user(request.user)
reversion.set_comment(comment)
if succieded:
msg = "Successfully added the following %i studies: \n%s" % (
len(succieded), "\n".join(succieded))
messages.add_message(request, messages.SUCCESS, ugettext(msg))
if warned:
msg = "Found already in db the following %i studies: \n%s" % (
len(warned), "\n".join(warned))
messages.add_message(request, messages.WARNING, ugettext(msg))
if failed:
msg = "Failed to fetch information on the following %i studies: \n%s" % (
len(failed), "\n".join(failed))
messages.add_message(request, messages.ERROR, ugettext(msg))
return HttpResponseRedirect('/lifespan/studies/')