def test_bulk_insert_should_throw_error_if_file_does_not_exist(self):
p = Patient()
p.save()
s = Sample(patient=p)
s.save()
self.assertRaises(
IOError, Clonotype.import_adaptive, s, '/fake/path/to/fake/file')
def migrate_library2sample_ingoringSpreadsheet(lib):
# check if its been migrated already
if Sample.objects.filter(sampleid=lib.sample_name).exists():
print "Library ", lib.library_code, "has been migrated already, skipping."
else:
#create an new samples.sample object
newsampleobj = Sample(organism=lib.organism, lifestage=lib.lifestage, growthphase=lib.growthphase, phenotype=lib.phenotype, genotype=lib.genotype, source=lib.source, sourcename=Source.objects.get(pk=1), sample_concentration=0, sample_volume=0, sample_quantity=0, author_modified=User.objects.get(username="******"))
newsampleobj.sampleid = 's' + lib.library_code
if lib.sample_name:
newsampleobj.sampleid = lib.sample_name
newsampleobj.date_created = lib.date_created
if lib.sample_notes != 'NA':
newsampleobj.sample_notes = lib.sample_notes
if lib.experiment_notes != 'NA':
newsampleobj.sample_notes = newsampleobj.sample_notes + ' ' + lib.experiment_notes
newsampleobj.collected_on = lib.collected_on
newsampleobj.collected_at = lib.collected_at
newsampleobj.collected_by = lib.collected_by
newsampleobj.treatment = lib.treatment
newsampleobj.collaborator = lib.collaborator
newsampleobj.sampletype = 'RNA'
#now save it
newsampleobj.save()
# save back sampleid into library table
lib.sampleid = newsampleobj
lib.save()
def test_import_adaptive_data_to_database(self):
# Make a test sample
p = Patient()
p.save()
s = Sample(patient=p)
s.save()
# Model can read in a file
Clonotype.import_adaptive(s, 'clonotypes/tests/data/test_adaptive.tsv')
all_clonotypes = Clonotype.objects.all()
self.assertEquals(len(all_clonotypes), 100)
def test_import_miTCR_to_database(self):
# Make a test sample
p = Patient()
p.save()
s = Sample(patient=p)
s.save()
# Model can read in a file
Clonotype.import_mitcr(s, 'clonotypes/tests/data/test_mitcr.txt')
all_clonotypes = Clonotype.objects.all()
self.assertEquals(len(all_clonotypes), 100)
self.fail('todo')
def make_fake_comparison_with_2_samples():
from clonotypes.models import AminoAcid
make_fake_patient_with_2_clonotypes()
p = Patient.objects.get()
s1 = Sample.objects.get()
s2 = Sample(patient=p, draw_date='2012-12-13', cell_type='cd4+')
s2.save()
# Make sure there's an overlapping amino_acid here
aa = AminoAcid.objects.all()[0]
r = aa.recombination_set.all()[0]
c = ClonotypeFactory(
sample=s2,
recombination = r
)
Comparison.default_from_samples([s1, s2])
def test_create_clonotypes_for_a_sample(self):
p = Patient()
p.save()
s = Sample(patient=p)
s.save()
r = RecombinationFactory()
c = Clonotype(
sample=s,
recombination=r,
frequency=9.336458E-6,
count=2,
)
c.save()
# Get all clonotypes from database
all_clonotypes = Clonotype.objects.all()
self.assertEqual(all_clonotypes[0], c)
def migrate_library2sample_ingoringSpreadsheet(lib):
# check if its been migrated already
if Sample.objects.filter(sampleid=lib.sample_name).exists():
print "Library ", lib.library_code, "has been migrated already, skipping."
else:
#create an new samples.sample object
newsampleobj = Sample(
organism=lib.organism,
lifestage=lib.lifestage,
growthphase=lib.growthphase,
phenotype=lib.phenotype,
genotype=lib.genotype,
source=lib.source,
sourcename=Source.objects.get(pk=1),
sample_concentration=0,
sample_volume=0,
sample_quantity=0,
author_modified=User.objects.get(username="******"))
newsampleobj.sampleid = 's' + lib.library_code
if lib.sample_name:
newsampleobj.sampleid = lib.sample_name
newsampleobj.date_created = lib.date_created
if lib.sample_notes != 'NA':
newsampleobj.sample_notes = lib.sample_notes
if lib.experiment_notes != 'NA':
newsampleobj.sample_notes = newsampleobj.sample_notes + ' ' + lib.experiment_notes
newsampleobj.collected_on = lib.collected_on
newsampleobj.collected_at = lib.collected_at
newsampleobj.collected_by = lib.collected_by
newsampleobj.treatment = lib.treatment
newsampleobj.collaborator = lib.collaborator
newsampleobj.sampletype = 'RNA'
#now save it
newsampleobj.save()
# save back sampleid into library table
lib.sampleid = newsampleobj
lib.save()
def add_oldstyle(request, username):
"""View for adding a new claim to old-style sample names. This is a nice
example of a view of the app “samples” which is *extended* in the institute
app. The template – in this case,
:file:`institute/templates/samples/list_claims.html` – overrides and extends the
default one, and adds a link to a URL listed in institute's URLconf and pointing
to this view function.
The important step is the template. This is the hook for your extensions.
You override the template from “samples” by creating a file called the same
in :file:`institute/templates/samples/`. Because ``TEMPLATE_DIRS`` and
``TEMPLATE_LOADERS`` are defined as recommended in
:doc:`/programming/settings`, it shadows its counterpart. By giving the
full path, you can still access the original. Thus, you may start your
template with
::
{% extends "samples/templates/samples/list_claims.html" %}
in order to extend it.
The `username` parameter of this view function is actually superfluous
because it must be the currently logged-in user anyway. But this way, we
don't get into trouble if a user happens to be called ``"add"``.
Additionally, the URLs become RESTful.
:param request: the current HTTP Request object
:param username: the name of the user whose claim this will be; it must be
the currently logged-in user
:type request: HttpRequest
:type username: unicode
:return:
the HTTP response object
:rtype: HttpResponse
"""
_ = ugettext
user = get_object_or_404(django.contrib.auth.models.User,
username=username)
if user != request.user:
raise permissions.PermissionError(
request.user,
_("You are not allowed to add a claim in another user's name."))
if request.method == "POST":
samples_form = SamplesForm(request.POST)
substrate_form = SubstrateForm(request.POST)
reviewer_form = ReviewerForm(request.POST)
if samples_form.is_valid() and substrate_form.is_valid(
) and reviewer_form.is_valid():
reviewer = reviewer_form.cleaned_data["reviewer"]
claim = SampleClaim(requester=user, reviewer=reviewer)
claim.save()
_ = lambda x: x
send_email(
_("Sample request from {requester}"),
_("""Hello {reviewer},
{requester} wants to become the new “currently responsible person”
of one or more samples. Please visit
{url}
for reviewing this request. If you don't want or cannot approve
the request, please contact {requester} directly and ask him or her
to withdraw the request.
JuliaBase.
"""), reviewer, {
"reviewer":
get_really_full_name(reviewer),
"requester":
get_really_full_name(user),
"url":
request.build_absolute_uri(
django.core.urlresolvers.reverse(
"samples.views.claim.show",
kwargs={"claim_id": claim.pk}))
})
_ = ugettext
samples = []
nobody = django.contrib.auth.models.User.objects.get(
username="******")
legacy = Topic.objects.get(name="Legacy")
now = datetime.datetime.now()
material, substrate_comments = substrate_form.cleaned_data[
"material"], substrate_form.cleaned_data["comments"]
for name in samples_form.cleaned_data["samples"]:
substrate = models.Substrate(operator=nobody,
timestamp=now,
material=material,
comments=substrate_comments)
substrate.save()
sample = Sample(name=name,
current_location="unknown",
currently_responsible_person=nobody,
topic=legacy)
sample.save()
sample.processes.add(substrate)
samples.append(sample)
claim.samples = samples
return utils.successful_response(
request,
_("Sample claim {id_} was successfully submitted.").format(
id_=claim.pk),
"samples.views.claim.show",
kwargs={"claim_id": claim.pk})
else:
samples_form = SamplesForm()
substrate_form = SubstrateForm()
reviewer_form = ReviewerForm()
return render(
request, "samples/add_claim_oldstyle.html", {
"title": _("Assert claim"),
"samples": samples_form,
"substrate": substrate_form,
"reviewer": reviewer_form
})
def load_orphan_sample(rowdic):
print rowdic
sampleid = rowdic['sampleid']
newsampleobj = Sample()
if Sample.objects.filter(sampleid=sampleid).exists():
newsampleobj = Sample.objects.get(sampleid=sampleid)
newsampleobj.sampleid = sampleid
# Things not in spread sheet but essential
newsampleobj.sampletype = "RNA"
newsampleobj.growthphase = Growthphase.objects.get(growthphase="log")
newsampleobj.phenotype = Phenotype.objects.get(phenotype="wildtype")
newsampleobj.author_modified = User.objects.get(username="******")
newsampleobj.sourcename = Source.objects.get(pk=1)
# Things From spread sheet
#
parentsampleid = "None"
if sampleid[-1].isdigit():
parentsampleid = "None"
else:
parentsampleid = rowdic['sampleid'][:-1]
print parentsampleid
newsampleobj.parent_sampleid = parentsampleid;
#
label_ontube = rowdic['oncap']
if rowdic['ontube']:
label_ontube = rowdic['oncap'] + ' / ' + rowdic['ontube']
newsampleobj.label_ontube = label_ontube
#
newsampleobj.genotype = Genotype.objects.get(genotype=rowdic['genotype'])
newsampleobj.lifestage = Lifestage.objects.get(lifestage=rowdic['stage'])
print rowdic['genus']
print rowdic['species']
print rowdic['strain']
print rowdic['dateisolated']
newsampleobj.organism = Organism.objects.get(genus=rowdic['genus'], species=rowdic['species'], strain=rowdic['strain'])
if rowdic['dateisolated']:
newsampleobj.collected_on = rowdic['dateisolated']
newsampleobj.collected_by = rowdic['sender']
newsampleobj.collected_by_emailid = rowdic['senderemailid']
newsampleobj.isolation_method = rowdic['isolationmethod']
newsampleobj.sample_dilution = rowdic['dilution']
if rowdic['daterecieved']:
newsampleobj.date_received = rowdic['daterecieved']
newsampleobj.sample_concentration = rowdic['concentration']
newsampleobj.sample_volume = rowdic['volume']
newsampleobj.sample_quantity = rowdic['quantity']
newsampleobj.biological_replicate_of = rowdic['replicate']
newsampleobj.freezer_location = rowdic['freezerlocation']
#
newsampleobj.sample_notes = rowdic['notesfromsender']
print rowdic['pi']
newsampleobj.collaborator = Collaborator.objects.get(lastname=rowdic['pi'])
print newsampleobj
newsampleobj.save()
sampleobj.biological_replicate_of = rowdic['replicate']
sampleobj.freezer_location = rowdic['freezerlocation']
sampleobj.sample_notes = libobj.sample_notes + "\n" + rowdic['notesfromsender']
#
parentsampleid = "None"
if sampleid[-1].isdigit():
parentsampleid = "None"
else:
parentsampleid = rowdic['sampleid'][:-1]
print parentsampleid
sampleobj.parent_sampleid = parentsampleid
sampleobj.author_modified = User.objects.get(username="******")
print sampleobj
sampleobj.save()
samples_loaded[sampleid]=sampleobj.id
for librarycode in librarycodes:
libobj = Library.objects.get(library_code=librarycode)
libobj.sampleid = sampleobj
libobj.save()
libraries_appended[librarycode]=libobj.id
else:
samples_notloaded[sampleid]= librarycode + " does not exist in Library table"
print "------------------------------------------------------------"
print "Samples not loaded:"
print samples_notloaded
print "Samples loaded:"
def load_orphan_sample(rowdic):
print rowdic
sampleid = rowdic['sampleid']
newsampleobj = Sample()
if Sample.objects.filter(sampleid=sampleid).exists():
newsampleobj = Sample.objects.get(sampleid=sampleid)
newsampleobj.sampleid = sampleid
# Things not in spread sheet but essential
newsampleobj.sampletype = "RNA"
newsampleobj.growthphase = Growthphase.objects.get(growthphase="log")
newsampleobj.phenotype = Phenotype.objects.get(phenotype="wildtype")
newsampleobj.author_modified = User.objects.get(username="******")
newsampleobj.sourcename = Source.objects.get(pk=1)
# Things From spread sheet
#
parentsampleid = "None"
if sampleid[-1].isdigit():
parentsampleid = "None"
else:
parentsampleid = rowdic['sampleid'][:-1]
print parentsampleid
newsampleobj.parent_sampleid = parentsampleid
#
label_ontube = rowdic['oncap']
if rowdic['ontube']:
label_ontube = rowdic['oncap'] + ' / ' + rowdic['ontube']
newsampleobj.label_ontube = label_ontube
#
newsampleobj.genotype = Genotype.objects.get(genotype=rowdic['genotype'])
newsampleobj.lifestage = Lifestage.objects.get(lifestage=rowdic['stage'])
print rowdic['genus']
print rowdic['species']
print rowdic['strain']
print rowdic['dateisolated']
newsampleobj.organism = Organism.objects.get(genus=rowdic['genus'],
species=rowdic['species'],
strain=rowdic['strain'])
if rowdic['dateisolated']:
newsampleobj.collected_on = rowdic['dateisolated']
newsampleobj.collected_by = rowdic['sender']
newsampleobj.collected_by_emailid = rowdic['senderemailid']
newsampleobj.isolation_method = rowdic['isolationmethod']
newsampleobj.sample_dilution = rowdic['dilution']
if rowdic['daterecieved']:
newsampleobj.date_received = rowdic['daterecieved']
newsampleobj.sample_concentration = rowdic['concentration']
newsampleobj.sample_volume = rowdic['volume']
newsampleobj.sample_quantity = rowdic['quantity']
newsampleobj.biological_replicate_of = rowdic['replicate']
newsampleobj.freezer_location = rowdic['freezerlocation']
#
newsampleobj.sample_notes = rowdic['notesfromsender']
print rowdic['pi']
newsampleobj.collaborator = Collaborator.objects.get(lastname=rowdic['pi'])
print newsampleobj
newsampleobj.save()
sampleobj.freezer_location = rowdic['freezerlocation']
sampleobj.sample_notes = libobj.sample_notes + "\n" + rowdic[
'notesfromsender']
#
parentsampleid = "None"
if sampleid[-1].isdigit():
parentsampleid = "None"
else:
parentsampleid = rowdic['sampleid'][:-1]
print parentsampleid
sampleobj.parent_sampleid = parentsampleid
sampleobj.author_modified = User.objects.get(username="******")
print sampleobj
sampleobj.save()
samples_loaded[sampleid] = sampleobj.id
for librarycode in librarycodes:
libobj = Library.objects.get(library_code=librarycode)
libobj.sampleid = sampleobj
libobj.save()
libraries_appended[librarycode] = libobj.id
else:
samples_notloaded[
sampleid] = librarycode + " does not exist in Library table"
print "------------------------------------------------------------"
print "Samples not loaded:"
print samples_notloaded
print "Samples loaded:"
def DONTtest_summary_should_redirect_if_a_new_sample_is_provided_in_form(self):
s2 = Sample(patient=self.p,cell_type="t", draw_date='1999-11-11')
s2.save()
url = "%s?clonofilter=1" % reverse('samples.views.summary', args=[s2.id])
self.assertRedirects(self.client.post(reverse('samples.views.summary', args=[self.s.id]),
{'sample': s2.id}), url)
def add_oldstyle(request, username):
"""View for adding a new claim to old-style sample names. This is a nice
example of a view of the app “samples” which is *extended* in the institute
app. The template – in this case,
:file:`institute/templates/samples/list_claims.html` – overrides and extends the
default one, and adds a link to a URL listed in institute's URLconf and pointing
to this view function.
The important step is the template. This is the hook for your extensions.
You override the template from “samples” by creating a file called the same
in :file:`institute/templates/samples/`. Because ``DIRS`` and ``loaders``
are defined as recommended in :doc:`/programming/settings`, it shadows its
counterpart. By giving the full path, you can still access the original.
Thus, you may start your template with
::
{% extends "samples/templates/samples/list_claims.html" %}
in order to extend it.
The `username` parameter of this view function is actually superfluous
because it must be the currently logged-in user anyway. But this way, we
don't get into trouble if a user happens to be called ``"add"``.
Additionally, the URLs become RESTful.
:param request: the current HTTP Request object
:param username: the name of the user whose claim this will be; it must be
the currently logged-in user
:type request: HttpRequest
:type username: unicode
:return:
the HTTP response object
:rtype: HttpResponse
"""
_ = ugettext
user = get_object_or_404(django.contrib.auth.models.User, username=username)
if user != request.user:
raise permissions.PermissionError(request.user, _("You are not allowed to add a claim in another user's name."))
if request.method == "POST":
samples_form = SamplesForm(request.POST)
substrate_form = SubstrateForm(request.POST)
reviewer_form = ReviewerForm(request.POST)
if samples_form.is_valid() and substrate_form.is_valid() and reviewer_form.is_valid():
reviewer = reviewer_form.cleaned_data["reviewer"]
claim = SampleClaim(requester=user, reviewer=reviewer)
claim.save()
_ = lambda x: x
send_email(_("Sample request from {requester}"),
_("""Hello {reviewer},
{requester} wants to become the new “currently responsible person”
of one or more samples. Please visit
{url}
for reviewing this request. If you don't want or cannot approve
the request, please contact {requester} directly and ask him or her
to withdraw the request.
JuliaBase.
"""), reviewer, {"reviewer": get_really_full_name(reviewer), "requester": get_really_full_name(user),
"url": request.build_absolute_uri(django.core.urlresolvers.reverse("samples.views.claim.show",
kwargs={"claim_id": claim.pk}))})
_ = ugettext
samples = []
nobody = django.contrib.auth.models.User.objects.get(username="******")
legacy = Topic.objects.get(name="Legacy")
now = datetime.datetime.now()
material, substrate_comments = substrate_form.cleaned_data["material"], substrate_form.cleaned_data["comments"]
for name in samples_form.cleaned_data["samples"]:
substrate = models.Substrate(operator=nobody, timestamp=now, material=material, comments=substrate_comments)
substrate.save()
sample = Sample(name=name, current_location="unknown", currently_responsible_person=nobody, topic=legacy)
sample.save()
sample.processes.add(substrate)
samples.append(sample)
claim.samples = samples
return utils.successful_response(request,
_("Sample claim {id_} was successfully submitted.").format(id_=claim.pk),
"samples.views.claim.show", kwargs={"claim_id": claim.pk})
else:
samples_form = SamplesForm()
substrate_form = SubstrateForm()
reviewer_form = ReviewerForm()
return render(request, "samples/add_claim_oldstyle.html", {"title": _("Assert claim"), "samples": samples_form,
"substrate": substrate_form, "reviewer": reviewer_form})