def motif_comparison_post(request, step):
"""Process motif comparison forms."""
try:
cur_site_insts = search.search_post_helper(request)
except:
message = "Please select at least one TF, species and experimental technique to search database."
messages.add_message(request, messages.ERROR, message)
return HttpResponseRedirect(
reverse(eval('motif_comparison_step%d' % step)))
if not cur_site_insts.filter(site_type='motif_associated'):
# If there is no motif-associated site, raise error
message = "No results found for selected TF and species"
messages.add_message(request, messages.ERROR, message)
return HttpResponseRedirect(
reverse(eval('motif_comparison_step%d' % step)))
# store search results
request.session['compare_step_%s' % step] = cur_site_insts
request.session.modified = True
if step == 1:
return HttpResponseRedirect(reverse(motif_comparison_step2))
else: # step2
# Render results
# Get motif_associated and non-motif_associated curation site instances
cur_site_insts_a = request.session['compare_step_1']
cur_site_insts_b = request.session['compare_step_2']
motif_a_reports = [
report.generate_view_reports_dict()
for report in motif_report.make_reports(cur_site_insts_a)
]
motif_a_ensemble_report = \
motif_report.make_ensemble_report(cur_site_insts_a).generate_view_reports_dict()
motif_b_reports = [
report.generate_view_reports_dict()
for report in motif_report.make_reports(cur_site_insts_b)
]
motif_b_ensemble_report = \
motif_report.make_ensemble_report(cur_site_insts_b).generate_view_reports_dict()
# clean session data from possible previous requests
# ???
request.session['permute_motif_a'] = None
request.session['permute_motif_b'] = None
request.session.modified = True
return render_to_response(
"motif_compare_results.html", {
'form_title': FORM_TITLES[2],
'form_description': FORM_DESCRIPTIONS[2],
'motif_a_reports': motif_a_reports,
'motif_b_reports': motif_b_reports,
'motif_a_ensemble_report': motif_a_ensemble_report,
'motif_b_ensemble_report': motif_b_ensemble_report,
},
context_instance=RequestContext(request))
def motif_comparison_post(request, step):
"""Process motif comparison forms."""
try:
cur_site_insts = search.search_post_helper(request)
except:
message = "Please select at least one TF, species and experimental technique to search database."
messages.add_message(request, messages.ERROR, message)
return HttpResponseRedirect(reverse(eval('motif_comparison_step%d' % step)))
if not cur_site_insts.filter(site_type='motif_associated'):
# If there is no motif-associated site, raise error
message = "No results found for selected TF and species"
messages.add_message(request, messages.ERROR, message)
return HttpResponseRedirect(reverse(eval('motif_comparison_step%d' % step)))
# store search results
request.session['compare_step_%s' % step] = cur_site_insts
request.session.modified = True
if step == 1:
return HttpResponseRedirect(reverse(motif_comparison_step2))
else: # step2
# Render results
# Get motif_associated and non-motif_associated curation site instances
cur_site_insts_a = request.session['compare_step_1']
cur_site_insts_b = request.session['compare_step_2']
motif_a_reports = [report.generate_view_reports_dict()
for report in motif_report.make_reports(cur_site_insts_a)]
motif_a_ensemble_report = \
motif_report.make_ensemble_report(cur_site_insts_a).generate_view_reports_dict()
motif_b_reports = [report.generate_view_reports_dict()
for report in motif_report.make_reports(cur_site_insts_b)]
motif_b_ensemble_report = \
motif_report.make_ensemble_report(cur_site_insts_b).generate_view_reports_dict()
# clean session data from possible previous requests
# ???
request.session['permute_motif_a'] = None
request.session['permute_motif_b'] = None
request.session.modified = True
return render_to_response("motif_compare_results.html",
{'form_title': FORM_TITLES[2],
'form_description': FORM_DESCRIPTIONS[2],
'motif_a_reports': motif_a_reports,
'motif_b_reports': motif_b_reports,
'motif_a_ensemble_report': motif_a_ensemble_report,
'motif_b_ensemble_report': motif_b_ensemble_report,},
context_instance=RequestContext(request))
def search_post(request):
"""Handler for database search request."""
def raise_validation_error(msg):
"""Check if all three steps have been submitted."""
messages.add_message(request, messages.ERROR, message)
return HttpResponseRedirect(reverse(search))
try:
cur_site_insts = search_post_helper(request)
# make reports
reports = motif_report.make_reports(cur_site_insts)
# make ensemble reports
ensemble_report = motif_report.make_ensemble_report(cur_site_insts)
if not reports:
# If no results found, go back to the search page.
message = "No search results that match your search criteria."
return raise_validation_error(message)
return render_to_response("search_results.html",
{
'title': "",
'description': """Search results can be
seen as individual reports (one report per
TF/species) or as ensemble reports
(multiple TF/species). """,
'all_cur_site_insts': [pk for report in reports
for pk in report.get_all_cur_site_insts_ids()],
'reports': [report.generate_browse_result_dict() for report in reports],
},
context_instance = RequestContext(request))
except:
message = "Please select at least one TF, species and experimental technique to search database."
return raise_validation_error(message)
def get_results_TF(request, type_, id):
"""GIven the type (TF or TF family) and the id of the object, return query
results and list TF/species that have binding site data for the selected TF
or TF family."""
if type_ == 'TF':
TFs = [models.TF.objects.get(TF_id=id)]
name = TFs[0].name
desc = TFs[0].description
elif type_ == 'TF_family':
# Get all TFs under that family
TF_family = models.TFFamily.objects.get(TF_family_id=id)
TFs = models.TF.objects.filter(family=TF_family).all()
name = TF_family.name
desc = TF_family.description
# get all curation-site-instance objects for browsed TFs
assert TFs
cur_site_insts = models.Curation_SiteInstance.objects.filter(
curation__TF__in=TFs)
# generate all reports
reports = motif_report.make_reports(cur_site_insts)
return render_to_response("browse_results.html",
{'title': name,
'description': desc,
'all_cur_site_insts': [pk for report in reports
for pk in report.get_all_cur_site_insts_ids()],
'reports': [report.generate_browse_result_dict() for report in reports],},
context_instance=RequestContext(request))
def get_results_tech(request, type_, id):
"""Given a technique category and an id describing that category object,
retrieve all curation-site-instance objects that have a technique with the
specified category."""
techniques = None
if type_ in ['binding', 'expression']:
techniques = models.ExperimentalTechnique.objects.filter(
preset_function=type_)
if type_ == 'binding':
title = 'Detection of binding'
desc = ''
else:
title = 'Assessment of expression'
desc = ''
elif type_ == 'binding_category':
category = models.ExperimentalTechniqueCategory.objects.get(
category_id=id)
techniques = models.ExperimentalTechnique.objects.filter(
categories=category, preset_function='binding')
title = category.name
desc = category.description
elif type_ == 'expression_category':
category = models.ExperimentalTechniqueCategory.objects.get(
category_id=id)
techniques = models.ExperimentalTechnique.objects.filter(
categories=category, preset_function='expression')
title = category.name
desc = category.description
elif type_ == 'technique':
techniques = models.ExperimentalTechnique.objects.filter(
technique_id=id)
# make sure the technique id is valid
assert techniques.count() > 0
title = techniques.all()[:1].get().name
desc = techniques.all()[:1].get().description
cur_site_insts = models.Curation_SiteInstance.objects.filter(
experimental_techniques=techniques)
# generate all reports
reports = motif_report.make_reports(cur_site_insts)
return render_to_response(
"browse_results.html", {
'title': title,
'description': desc,
'reports':
[report.generate_browse_result_dict() for report in reports]
},
context_instance=RequestContext(request))
def view_reports(request):
"""Handler for the post request, performed on browse by TF/species/technique
page. Given the list of motif-associated and non-motif-associated
curation-site-instance ids, they are grouped by TF and species, and
rendered"""
# make sure that it is a POST request
if not request.POST: return HttpResponseRedirect(reverse(base.views.home))
cur_site_inst_ids = request.POST["csi_list"].strip().split(',')
# get all curation-site-instances
cur_site_insts = models.Curation_SiteInstance.objects.filter(pk__in=cur_site_inst_ids)
# integrate non-motif: if True, the experimental evidence and regulation
# information from non-motif associated sites are integrated into the report
integrate_non_motif = bool("integrate_non_motif" in request.POST)
# Check if non-motif site integration is requested
if integrate_non_motif:
reports = motif_report.make_reports(cur_site_insts)
else:
# if not, exclude non-motif-associated sites before generating reports
reports = motif_report.make_reports(cur_site_insts.exclude(site_type='non_motif_associated'))
# combine reports into ensemble report
ensemble_report = motif_report.merge_reports(reports)
#ensemble_report = motif_report.make_ensemble_report(cur_site_insts)
return render_to_response("view_reports.html",
{
"reports": [report.generate_view_reports_dict()
for report in reports],
"ensemble_report": ensemble_report.generate_view_reports_dict(),
"cur_site_insts": ','.join(map(lambda x: str(x.pk), cur_site_insts)),
"integrate_non_motif": integrate_non_motif,
},
context_instance=RequestContext(request))
def get_results_taxonomy(request, taxid):
"""Given a taxonomy id, find all species under that taxon, and return
results for those species"""
def get_all_sp(taxid):
"""Given a taxon t, return all species (leaves) of the phylogeny where t
is the root of the tree."""
all_sp = []
Q = Queue.Queue()
Q.put(models.Taxonomy.objects.get(pk=taxid))
while not Q.empty():
node = Q.get()
children = node.taxonomy_set.all()
if children:
for c in children:
Q.put(c)
else:
all_sp.append(node)
return all_sp
# get all species
all_species = get_all_sp(taxid)
# get all curation-site-instance objects for browsed taxon
cur_site_insts = models.Curation_SiteInstance.objects.filter(
site_instance__genome__taxonomy__in=all_species)
# generate all reports
reports = motif_report.make_reports(cur_site_insts)
return render_to_response("browse_results.html", {
'title':
models.Taxonomy.objects.get(pk=taxid).name,
'description':
'',
'all_cur_site_insts': [
pk for report in reports
for pk in report.get_all_cur_site_insts_ids()
],
'reports':
[report.generate_browse_result_dict() for report in reports],
},
context_instance=RequestContext(request))
def search_post(request):
"""Handler for database search request."""
def raise_validation_error(msg):
"""Check if all three steps have been submitted."""
messages.add_message(request, messages.ERROR, message)
return HttpResponseRedirect(reverse(search))
try:
cur_site_insts = search_post_helper(request)
# make reports
reports = motif_report.make_reports(cur_site_insts)
# make ensemble reports
ensemble_report = motif_report.make_ensemble_report(cur_site_insts)
if not reports:
# If no results found, go back to the search page.
message = "No search results that match your search criteria."
return raise_validation_error(message)
return render_to_response("search_results.html", {
'title':
"",
'description':
"""Search results can be
seen as individual reports (one report per
TF/species) or as ensemble reports
(multiple TF/species). """,
'all_cur_site_insts': [
pk for report in reports
for pk in report.get_all_cur_site_insts_ids()
],
'reports':
[report.generate_browse_result_dict() for report in reports],
},
context_instance=RequestContext(request))
except:
message = "Please select at least one TF, species and experimental technique to search database."
return raise_validation_error(message)