def phenotips_edit_handler(request, project_guid, patient_id):
"""Request the PhenoTips Edit page for the given patient_id, and forwards PhenoTips' response to the client.
Args:
request: Django HTTP request object
project_guid (string): project GUID for the seqr project containing this individual
patient_id (string): PhenoTips internal patient id
"""
# query string forwarding needed for PedigreeEditor button
query_string = request.META["QUERY_STRING"]
url = "/bin/edit/data/{patient_id}?{query_string}".format(
patient_id=patient_id, query_string=query_string)
project = Project.objects.get(guid=project_guid)
check_permissions(project, request.user, CAN_EDIT)
auth_tuple = _get_phenotips_username_and_password(
request.user, project, permissions_level=CAN_EDIT)
return proxy_request(request,
url,
headers={},
auth_tuple=auth_tuple,
host=settings.PHENOTIPS_SERVER)
def _phenotips_view_handler(request,
project_guid,
individual_guid,
url_template,
permission_level=CAN_VIEW):
"""Requests the PhenoTips PDF for the given patient_id, and forwards PhenoTips' response to the client.
Args:
request: Django HTTP request object
project_guid (string): project GUID for the seqr project containing this individual
individual_guid (string): individual GUID for the seqr individual corresponding to the desired patient
"""
project = Project.objects.get(guid=project_guid)
check_permissions(project, request.user, CAN_VIEW)
individual = Individual.objects.get(guid=individual_guid)
_create_patient_if_missing(project, individual)
_set_phenotips_patient_id_if_missing(project, individual)
# query string forwarding needed for PedigreeEditor button
query_string = request.META["QUERY_STRING"]
url = url_template.format(patient_id=individual.phenotips_patient_id,
query_string=query_string)
auth_tuple = _get_phenotips_username_and_password(
request.user, project, permissions_level=permission_level)
return proxy_request(request,
url,
headers={},
auth_tuple=auth_tuple,
host=settings.PHENOTIPS_SERVER)
def update_family_pedigree_image(request, family_guid):
"""Updates the specified field in the Family model.
Args:
family_guid (string): GUID of the family.
"""
family = Family.objects.get(guid=family_guid)
# check permission
check_permissions(family.project, request.user, CAN_EDIT)
if len(request.FILES) == 0:
pedigree_image = None
elif len(request.FILES) > 1:
return create_json_response({},
status=400,
reason='Received {} files'.format(
len(request.FILES)))
else:
pedigree_image = request.FILES.values()[0]
update_seqr_model(family, pedigree_image=pedigree_image)
return create_json_response(
{family.guid: _get_json_for_family(family, request.user)})
def delete_mme_submission(request, individual_guid):
"""
Create or update the submission for the given individual.
"""
individual = Individual.objects.get(guid=individual_guid)
project = individual.family.project
check_permissions(project, request.user)
if individual.mme_deleted_date:
return create_json_response(
{}, status=402, reason='Matchmaker submission has already been deleted for {}'.format(individual.individual_id),
)
matchbox_id = individual.mme_submitted_data['patient']['id']
response = requests.delete(url=MME_DELETE_INDIVIDUAL_URL, headers=MME_HEADERS, data=json.dumps({'id': matchbox_id}))
if response.status_code != 200:
try:
response_json = response.json()
except Exception:
response_json = {}
return create_json_response(response_json, status=response.status_code, reason=response.content)
deleted_date = datetime.now()
individual.mme_deleted_date = deleted_date
individual.mme_deleted_by = request.user
individual.save()
return create_json_response({'individualsByGuid': {individual_guid: {'mmeDeletedDate': deleted_date}}})
def create_saved_variant_handler(request):
variant_json = json.loads(request.body)
family_guid = variant_json.pop('familyGuid')
non_variant_json = {
k: variant_json.pop(k, None) for k in ['searchHash', 'tags', 'functionalData', 'notes', 'note', 'submitToClinvar']
}
family = Family.objects.get(guid=family_guid)
check_permissions(family.project, request.user, CAN_VIEW)
xpos = variant_json['xpos']
ref = variant_json['ref']
alt = variant_json['alt']
# TODO remove project field from saved variants
saved_variant = SavedVariant.objects.create(
xpos=xpos,
xpos_start=xpos,
xpos_end=xpos + len(ref) - 1,
ref=ref,
alt=alt,
family=family,
project=family.project,
saved_variant_json=json.dumps(variant_json)
)
if non_variant_json.get('note'):
_create_variant_note(saved_variant, non_variant_json, request.user)
elif non_variant_json.get('tags'):
_create_new_tags(saved_variant, non_variant_json, request.user)
variant_json.update(get_json_for_saved_variant(saved_variant, add_tags=True, project_guid=family.project.guid))
return create_json_response({
'savedVariantsByGuid': {saved_variant.guid: variant_json},
})
def delete_mme_submission(request, individual_guid):
"""
Create or update the submission for the given individual.
"""
individual = Individual.objects.get(guid=individual_guid)
project = individual.family.project
check_permissions(project, request.user)
if individual.mme_deleted_date:
return create_json_response(
{}, status=402, reason='Matchmaker submission has already been deleted for {}'.format(individual.individual_id),
)
matchbox_id = individual.mme_submitted_data['patient']['id']
response = requests.delete(url=MME_DELETE_INDIVIDUAL_URL, headers=MME_HEADERS, data=json.dumps({'id': matchbox_id}))
if response.status_code != 200:
try:
response_json = response.json()
except Exception:
response_json = {}
return create_json_response(response_json, status=response.status_code, reason=response.content)
deleted_date = datetime.now()
individual.mme_deleted_date = deleted_date
individual.mme_deleted_by = request.user
individual.save()
for saved_result in MatchmakerResult.objects.filter(individual=individual):
if not (saved_result.we_contacted or saved_result.host_contacted or saved_result.comments):
saved_result.delete()
return create_json_response({'individualsByGuid': {individual_guid: {'mmeDeletedDate': deleted_date}}})
def get_individual_mme_matches(request, individual_guid):
"""
Looks for matches for the given individual. Expects a single patient (MME spec) in the POST
data field under key "patient_data"
Args:
project_id,indiv_id and POST all data in POST under key "patient_data"
Returns:
Status code and results
"""
individual = Individual.objects.get(guid=individual_guid)
project = individual.family.project
check_permissions(project, request.user)
results = MatchmakerResult.objects.filter(individual=individual)
saved_variants = get_json_for_saved_variants(
SavedVariant.objects.filter(family=individual.family), add_tags=True, add_details=True,
project=project, user=request.user)
gene_ids = set()
for variant in saved_variants:
gene_ids.update(variant['transcripts'].keys())
return _parse_mme_results(
individual, results, request.user, additional_genes=gene_ids, response_json={
'savedVariantsByGuid': {variant['variantGuid']: variant for variant in saved_variants}})
def update_individual_handler(request, individual_guid):
"""Updates a single field in an Individual record.
Args:
request (object): Django HTTP Request object.
individual_guid (string): GUID of the Individual.
Request:
body should be a json dictionary like: { 'value': xxx }
Response:
json dictionary representing the updated individual like:
{
<individualGuid> : {
individualId: xxx,
sex: xxx,
affected: xxx,
...
}
}
"""
individual = Individual.objects.get(guid=individual_guid)
project = individual.family.project
check_permissions(project, request.user, CAN_EDIT)
request_json = json.loads(request.body)
update_individual_from_json(individual, request_json, user=request.user, allow_unknown_keys=True)
return create_json_response({
individual.guid: _get_json_for_individual(individual, request.user)
})
def update_family_assigned_analyst(request, family_guid):
"""Updates the specified field in the Family model.
Args:
family_guid (string): GUID of the family.
"""
family = Family.objects.get(guid=family_guid)
check_permissions(family.project, request.user, CAN_EDIT)
request_json = json.loads(request.body)
assigned_analyst_username = request_json.get('assigned_analyst_username')
if assigned_analyst_username:
try:
assigned_analyst = User.objects.get(
username=assigned_analyst_username)
except Exception:
return create_json_response({},
status=400,
reason="specified user does not exist")
else:
assigned_analyst = None
update_seqr_model(family, assigned_analyst=assigned_analyst)
return create_json_response(
{family.guid: _get_json_for_family(family, request.user)})
def update_individual_hpo_terms(request, individual_guid):
individual = Individual.objects.get(guid=individual_guid)
project = individual.family.project
check_permissions(project, request.user, CAN_EDIT)
features = json.loads(request.body)
_create_patient_if_missing(project, individual)
patient_json = _get_patient_data(project, individual)
patient_json["features"] = features
patient_json_string = json.dumps(patient_json)
url = _phenotips_patient_url(individual)
auth_tuple = _get_phenotips_uname_and_pwd_for_project(project.phenotips_user_id, read_only=False)
_make_api_call('PUT', url, data=patient_json_string, auth_tuple=auth_tuple, expected_status_code=204)
phenotips_patient_id = patient_json['id']
phenotips_eid = patient_json.get('external_id')
update_seqr_model(
individual,
phenotips_data=json.dumps(patient_json),
phenotips_patient_id=phenotips_patient_id,
phenotips_eid=phenotips_eid)
return create_json_response({
individual.guid: {
'phenotipsData': patient_json,
'phenotipsPatientId': phenotips_patient_id,
'phenotipsEid': phenotips_eid
}
})
def update_family_field_handler(request, family_guid, field_name):
"""Updates the specified field in the Family model.
Args:
family_guid (string): GUID of the family.
field_name (string): Family model field name to update
"""
family = Family.objects.get(guid=family_guid)
# check permission
project = family.project
check_permissions(project, request.user, CAN_EDIT)
request_json = json.loads(request.body)
if "value" not in request_json:
raise ValueError("Request is missing 'value' key: %s" %
(request.body, ))
value = request_json['value']
family_json = {field_name: value}
update_family_from_json(family, family_json)
_deprecated_update_original_family_field(project, family, field_name,
value)
return create_json_response(
{family.guid: _get_json_for_family(family, request.user)})
def update_variant_tags_handler(request, variant_guids):
request_json = json.loads(request.body)
family_guid = request_json.pop('familyGuid')
family = Family.objects.get(guid=family_guid)
check_permissions(family.project, request.user, CAN_VIEW)
all_variant_guids = set(variant_guids.split(','))
saved_variants = SavedVariant.objects.filter(guid__in=all_variant_guids)
if len(saved_variants) != len(all_variant_guids):
error = 'Unable to find the following variant(s): {}'.format(
', '.join([guid for guid in all_variant_guids if guid not in {sv.guid for sv in saved_variants}]))
return create_json_response({'error': error}, status=400, reason=error)
deleted_tag_guids = _delete_removed_tags(saved_variants, all_variant_guids, request_json.get('tags', []))
created_tags = _create_new_tags(saved_variants, request_json, request.user)
tag_updates = {tag['tagGuid']: tag for tag in get_json_for_variant_tags(created_tags)}
tag_updates.update({guid: None for guid in deleted_tag_guids})
return create_json_response({
'savedVariantsByGuid': {saved_variant.guid: {
'tagGuids': [t.guid for t in saved_variant.varianttag_set.all()],
} for saved_variant in saved_variants},
'variantTagsByGuid': tag_updates,
})
def create_saved_variant_handler(request):
variant_json = json.loads(request.body)
family_guid = variant_json['familyGuid']
family = Family.objects.get(guid=family_guid)
check_permissions(family.project, request.user, CAN_VIEW)
if isinstance(variant_json['variant'], list):
# are compound hets
saved_variants = []
for single_variant_json in variant_json['variant']:
saved_variant, created = SavedVariant.objects.get_or_create(
**_get_parsed_variant_args(single_variant_json, family))
if created:
saved_variant.saved_variant_json = single_variant_json
saved_variant.save()
saved_variants.append(saved_variant)
else:
saved_variant = SavedVariant.objects.create(
saved_variant_json=variant_json['variant'],
**_get_parsed_variant_args(variant_json['variant'], family))
saved_variants = [saved_variant]
if variant_json.get('note'):
_create_variant_note(saved_variants, variant_json, request.user)
elif variant_json.get('tags'):
_create_new_tags(saved_variants, variant_json, request.user)
return create_json_response(
get_json_for_saved_variants_with_tags(saved_variants,
add_details=True))
def delete_variant_note_handler(request, variant_guids, note_guid):
variant_guids = variant_guids.split(',')
note = VariantNote.objects.get(guid=note_guid)
projects = {
saved_variant.family.project
for saved_variant in note.saved_variants.all()
}
for project in projects:
check_permissions(project, request.user, CAN_VIEW)
note.delete()
saved_variants_by_guid = {}
for saved_variant in SavedVariant.objects.filter(guid__in=variant_guids):
notes = saved_variant.variantnote_set.all()
saved_variants_by_guid[saved_variant.guid] = {
'noteGuids': [n.guid for n in notes]
}
if not notes:
if not saved_variant.varianttag_set.count() > 0:
saved_variant.delete()
saved_variants_by_guid[saved_variant.guid] = None
return create_json_response({
'savedVariantsByGuid': saved_variants_by_guid,
'variantNotesByGuid': {
note_guid: None
},
})
def update_variant_tags_handler(request, variant_guid):
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.project, request.user, CAN_EDIT)
request_json = json.loads(request.body)
updated_tags = request_json.get('tags', [])
updated_functional_data = request_json.get('functionalData', [])
# Update tags
existing_tag_guids = [tag['tagGuid'] for tag in updated_tags if tag.get('tagGuid')]
new_tags = [tag for tag in updated_tags if not tag.get('tagGuid')]
for tag in saved_variant.varianttag_set.exclude(guid__in=existing_tag_guids):
delete_seqr_model(tag)
for tag in new_tags:
variant_tag_type = VariantTagType.objects.get(
Q(name=tag['name']),
Q(project=saved_variant.project) | Q(project__isnull=True)
)
create_seqr_model(
VariantTag,
saved_variant=saved_variant,
variant_tag_type=variant_tag_type,
search_parameters=request_json.get('searchParameters'),
created_by=request.user,
)
# Update functional data
existing_functional_guids = [tag['tagGuid'] for tag in updated_functional_data if tag.get('tagGuid')]
for tag in saved_variant.variantfunctionaldata_set.exclude(guid__in=existing_functional_guids):
delete_seqr_model(tag)
for tag in updated_functional_data:
if tag.get('tagGuid'):
tag_model = VariantFunctionalData.objects.get(
guid=tag.get('tagGuid'),
functional_data_tag=tag.get('name'),
saved_variant=saved_variant
)
update_model_from_json(tag_model, tag, allow_unknown_keys=True)
else:
create_seqr_model(
VariantFunctionalData,
saved_variant=saved_variant,
functional_data_tag=tag.get('name'),
metadata=tag.get('metadata'),
search_parameters=request_json.get('searchParameters'),
created_by=request.user,
)
return create_json_response({
variant_guid: {
'tags': [get_json_for_variant_tag(tag) for tag in saved_variant.varianttag_set.all()],
'functionalData': [get_json_for_variant_functional_data(tag) for tag in saved_variant.variantfunctionaldata_set.all()]
}
})
def phenotips_edit_handler(request, project_guid, patient_id):
"""Request the PhenoTips Edit page for the given patient_id, and forwards PhenoTips' response to the client.
Args:
request: Django HTTP request object
project_guid (string): project GUID for the seqr project containing this individual
patient_id (string): PhenoTips internal patient id
"""
# query string forwarding needed for PedigreeEditor button
query_string = request.META["QUERY_STRING"]
url = "/bin/edit/data/%(patient_id)s?%(query_string)s" % locals()
project = Project.objects.get(guid=project_guid)
check_permissions(project, request.user, CAN_EDIT)
auth_tuple = _get_phenotips_username_and_password(request.user, project, permissions_level=CAN_EDIT)
#if 'current_phenotips_session' not in request.session:
# phenotips_session = requests.Session()
# request.session['current_phenotips_session'] = pickle.dumps(phenotips_session)
#else:
# phenotips_session = pickle.loads(request.session['current_phenotips_session'])
return _send_request_to_phenotips('GET', url, scheme=request.scheme, auth_tuple=auth_tuple) #, session=phenotips_session)
def update_individual_hpo_terms(request, individual_guid):
individual = Individual.objects.get(guid=individual_guid)
project = individual.family.project
check_permissions(project, request.user, CAN_EDIT)
features = json.loads(request.body)
_create_patient_if_missing(project, individual)
patient_json = _get_patient_data(project, individual)
patient_json["features"] = features
patient_json_string = json.dumps(patient_json)
url = phenotips_patient_url(individual)
auth_tuple = get_phenotips_uname_and_pwd_for_project(project.phenotips_user_id, read_only=False)
make_phenotips_api_call('PUT', url, data=patient_json_string, auth_tuple=auth_tuple, expected_status_code=204)
phenotips_patient_id = patient_json['id']
phenotips_eid = patient_json.get('external_id')
individual.phenotips_data = json.dumps(patient_json)
individual.phenotips_patient_id = phenotips_patient_id
individual.phenotips_eid = phenotips_eid
individual.save()
return create_json_response({
individual.guid: {
'phenotipsData': patient_json,
'phenotipsPatientId': phenotips_patient_id,
'phenotipsEid': phenotips_eid
}
})
def _get_project_details(project, user):
check_permissions(project, user)
project_json = _get_json_for_project(project, user)
families_by_guid, individuals_by_guid, samples_by_guid, analysis_groups_by_guid, locus_lists_by_guid = get_project_child_entities(
project, user)
project_json.update({
'hasGeneSearch':
True,
'locusListGuids':
locus_lists_by_guid.keys(),
'variantTagTypes':
get_project_variant_tag_types(project),
'variantFunctionalTagTypes':
get_json_for_variant_functional_data_tag_types(),
})
return {
'projectsByGuid': {
project.guid: project_json
},
'familiesByGuid': families_by_guid,
'individualsByGuid': individuals_by_guid,
'samplesByGuid': samples_by_guid,
'locusListsByGuid': locus_lists_by_guid,
'analysisGroupsByGuid': analysis_groups_by_guid,
}
def create_variant_note_handler(request, variant_guids):
request_json = json.loads(request.body)
save_as_gene_note = request_json.get('saveAsGeneNote')
family_guid = request_json.pop('familyGuid')
family = Family.objects.get(guid=family_guid)
check_permissions(family.project, request.user, CAN_VIEW)
all_variant_guids = variant_guids.split(',')
saved_variants = SavedVariant.objects.filter(guid__in=all_variant_guids)
if len(saved_variants) != len(all_variant_guids):
error = 'Unable to find the following variant(s): {}'.format(', '.join(
[
guid for guid in all_variant_guids
if guid not in {sv.guid
for sv in saved_variants}
]))
return create_json_response({'error': error}, status=400, reason=error)
# update saved_variants
note = _create_variant_note(saved_variants, request_json, request.user)
note_json = get_json_for_variant_note(note, add_variant_guids=False)
note_json['variantGuids'] = all_variant_guids
response = {
'savedVariantsByGuid': {
saved_variant.guid: {
'noteGuids':
[n.guid for n in saved_variant.variantnote_set.all()]
}
for saved_variant in saved_variants
},
'variantNotesByGuid': {
note.guid: note_json
},
}
if save_as_gene_note:
main_transcript_id = saved_variants[
0].selected_main_transcript_id or saved_variants[
0].saved_variant_json['mainTranscriptId']
gene_id = next(
(gene_id for gene_id, transcripts in saved_variants[0].
saved_variant_json['transcripts'].items() if any(
t['transcriptId'] == main_transcript_id
for t in transcripts)), None) if main_transcript_id else None
GeneNote.objects.create(
note=request_json.get('note'),
gene_id=gene_id,
created_by=request.user,
)
response['genesById'] = {
gene_id: {
'notes':
get_json_for_gene_notes_by_gene_id([gene_id],
request.user)[gene_id],
}
}
return create_json_response(response)
def update_variant_main_transcript(request, variant_guid, transcript_id):
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.family.project, request.user, CAN_EDIT)
saved_variant.selected_main_transcript_id = transcript_id
saved_variant.save()
return create_json_response({'savedVariantsByGuid': {variant_guid: {'selectedMainTranscriptId': transcript_id}}})
def delete_variant_note_handler(request, variant_guid, note_guid):
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.project, request.user, CAN_EDIT)
note = VariantNote.objects.get(guid=note_guid, saved_variant=saved_variant)
delete_seqr_model(note)
return create_json_response({variant_guid: {
'notes': [get_json_for_variant_note(tag) for tag in saved_variant.variantnote_set.all()]
}})
def delete_variant_note_handler(request, variant_guid, note_guid):
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.project, request.user, CAN_VIEW)
note = VariantNote.objects.get(guid=note_guid, saved_variant=saved_variant)
delete_seqr_model(note)
return create_json_response({'savedVariantsByGuid': {variant_guid: {
'notes': [get_json_for_variant_note(tag) for tag in saved_variant.variantnote_set.all()]
}}})
def create_variant_note_handler(request, variant_guid):
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.project, request.user, CAN_VIEW)
_create_variant_note(saved_variant, json.loads(request.body), request.user)
return create_json_response({'savedVariantsByGuid': {variant_guid: {
'notes': [get_json_for_variant_note(tag) for tag in saved_variant.variantnote_set.all()]
}}})
def update_project_categories_handler(request, project_guid):
"""Update ProjectCategories for the given project.
Args:
project_guid (string): GUID of the project that should be updated
HTTP POST
Request body - should contain the following json structure:
{
'form' : {
'categories': a list of category GUIDs for the categories assigned to the given project
}
}
Response body - will contain the following structure, representing the updated project,
as well all categories in seqr:
{
'projectsByGuid': {
<projectGuid1> : { ... <project key-value pairs> ... }
}
'projectCategoriesByGuid': {
<projectCategoryGuid1> : { ... <category key-value pairs> ... }
<projectCategoryGuid2> : { ... <category key-value pairs> ... }
}
}
"""
project = Project.objects.get(guid=project_guid)
# check permissions
check_permissions(project, request.user, CAN_EDIT)
request_json = json.loads(request.body)
if 'form' not in request_json:
return create_json_response(
{},
status=400,
reason="Invalid request: 'form' not in request_json")
form_data = request_json['form']
# project categories according to the UI
current_category_guids = set(form_data['categories'])
project_categories_by_guid = _update_project_categories(
project, request.user, current_category_guids)
projects_by_guid = {
project.guid: _get_json_for_project(project, request.user)
}
return create_json_response({
'projectsByGuid':
projects_by_guid,
'projectCategoriesByGuid':
project_categories_by_guid,
})
def update_variant_tags_handler(request, variant_guid):
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.family.project, request.user, CAN_VIEW)
request_json = json.loads(request.body)
updated_tags = request_json.get('tags', [])
updated_functional_data = request_json.get('functionalData', [])
# Update tags
existing_tag_guids = [
tag['tagGuid'] for tag in updated_tags if tag.get('tagGuid')
]
saved_variant.varianttag_set.exclude(guid__in=existing_tag_guids).delete()
_create_new_tags(saved_variant, request_json, request.user)
# Update functional data
existing_functional_guids = [
tag['tagGuid'] for tag in updated_functional_data if tag.get('tagGuid')
]
saved_variant.variantfunctionaldata_set.exclude(
guid__in=existing_functional_guids).delete()
for tag in updated_functional_data:
if tag.get('tagGuid'):
tag_model = VariantFunctionalData.objects.get(
guid=tag.get('tagGuid'),
functional_data_tag=tag.get('name'),
saved_variant=saved_variant)
update_model_from_json(tag_model, tag, allow_unknown_keys=True)
else:
VariantFunctionalData.objects.create(
saved_variant=saved_variant,
functional_data_tag=tag.get('name'),
metadata=tag.get('metadata'),
search_hash=request_json.get('searchHash'),
created_by=request.user,
)
return create_json_response({
'savedVariantsByGuid': {
variant_guid: {
'tags': [
get_json_for_variant_tag(tag)
for tag in saved_variant.varianttag_set.all()
],
'functionalData': [
get_json_for_variant_functional_data(tag)
for tag in saved_variant.variantfunctionaldata_set.all()
]
}
}
})
def update_mme_submission(request, individual_guid):
"""
Create or update the submission for the given individual.
"""
individual = Individual.objects.get(guid=individual_guid)
check_permissions(individual.family.project, request.user)
submission_json = json.loads(request.body)
submission_json.pop('individualGuid', {})
phenotypes = submission_json.pop('phenotypes', [])
gene_variants = submission_json.pop('geneVariants', [])
if not phenotypes and not gene_variants:
return create_json_response({}, status=400, reason='Genotypes or phentoypes are required')
if not submission_json.get('patient', {}).get('id'):
return create_json_response({}, status=400, reason='Patient id is required')
genomic_features = []
for gene_variant in gene_variants:
if not gene_variant.get('geneId'):
return create_json_response({}, status=400, reason='Gene id is required for genomic features')
feature = {'gene': {'id': gene_variant['geneId']}}
if 'numAlt' in gene_variant:
feature['zygosity'] = gene_variant['numAlt'] % 2
if gene_variant.get('pos'):
feature['variant'] = {
'alternateBases': gene_variant['alt'],
'referenceBases': gene_variant['ref'],
'referenceName': gene_variant['chrom'],
'start': gene_variant['pos'],
'assembly': GENOME_VERSION_LOOKUP[gene_variant['genomeVersion']],
}
genomic_features.append(feature)
submission_json['patient']['genomicFeatures'] = genomic_features
submission_json['patient']['features'] = phenotypes
response = requests.post(url=MME_ADD_INDIVIDUAL_URL, headers=MME_HEADERS, data=json.dumps(submission_json))
if response.status_code not in (200, 409):
try:
response_json = response.json()
except Exception:
response_json = {}
return create_json_response(response_json, status=response.status_code, reason=response.content)
submitted_date = datetime.now()
individual.mme_submitted_data = submission_json
individual.mme_submitted_date = submitted_date
individual.mme_deleted_date = None
individual.mme_deleted_by = None
individual.save()
# search for new matches
return _search_individual_matches(individual, request.user)
def update_variant_note_handler(request, variant_guid, note_guid):
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.project, request.user, CAN_VIEW)
note = VariantNote.objects.get(guid=note_guid, saved_variant=saved_variant)
request_json = json.loads(request.body)
update_model_from_json(note, request_json, allow_unknown_keys=True)
return create_json_response({'savedVariantsByGuid': {variant_guid: {
'notes': [get_json_for_variant_note(tag) for tag in saved_variant.variantnote_set.all()]
}}})
def update_variant_note_handler(request, variant_guid, note_guid):
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.project, request.user, CAN_EDIT)
note = VariantNote.objects.get(guid=note_guid, saved_variant=saved_variant)
request_json = json.loads(request.body)
update_model_from_json(note, request_json, allow_unknown_keys=True)
return create_json_response({variant_guid: {
'notes': [get_json_for_variant_note(tag) for tag in saved_variant.variantnote_set.all()]
}})
def update_project_handler(request, project_guid):
"""Update project metadata - including one or more of these fields: name, description
Args:
project_guid (string): GUID of the project that should be updated
HTTP POST
Request body - should contain the following json structure:
{
'form' : {
'name': <project name>,
'description': <project description>,
}
}
Response body - will contain the following structure, representing the updated project:
{
'projectsByGuid': {
<projectGuid1> : { ... <project key-value pairs> ... }
}
}
"""
project = Project.objects.get(guid=project_guid)
check_permissions(project, request.user, CAN_EDIT)
request_json = json.loads(request.body)
if 'form' not in request_json:
return create_json_response(
{},
status=400,
reason="Invalid request: 'form' not in request_json")
form_data = request_json['form']
if 'name' in form_data:
project.name = form_data.get('name')
project.save()
if 'description' in form_data:
project.description = form_data.get('description')
project.save()
# keep new seqr.Project model in sync with existing xbrowse_server.base.models - TODO remove this code after transition to new schema is finished
_deprecated_update_original_project(project)
return create_json_response({
'projectsByGuid': {
project.guid: _get_json_for_project(project, request.user)
},
})
def search_individual_mme_matches(request, individual_guid):
"""
Looks for matches for the given individual. Expects a single patient (MME spec) in the POST
data field under key "patient_data"
Args:
project_id,indiv_id and POST all data in POST under key "patient_data"
Returns:
Status code and results
"""
individual = Individual.objects.get(guid=individual_guid)
project = individual.family.project
check_permissions(project, request.user)
return _search_individual_matches(individual, request.user)
def search_individual_mme_matches(request, individual_guid):
"""
Looks for matches for the given individual. Expects a single patient (MME spec) in the POST
data field under key "patient_data"
Args:
project_id,indiv_id and POST all data in POST under key "patient_data"
Returns:
Status code and results
"""
individual = Individual.objects.get(guid=individual_guid)
project = individual.family.project
check_permissions(project, request.user)
return _search_individual_matches(individual, request.user)
def update_variant_note_handler(request, variant_guids, note_guid):
note = VariantNote.objects.get(guid=note_guid)
projects = {saved_variant.family.project for saved_variant in note.saved_variants.all()}
for project in projects:
check_permissions(project, request.user, CAN_VIEW)
request_json = json.loads(request.body)
update_model_from_json(note, request_json, allow_unknown_keys=True)
note_json = get_json_for_variant_note(note, add_variant_guids=False)
note_json['variantGuids'] = variant_guids.split(',')
return create_json_response({
'variantNotesByGuid': {note.guid: note_json},
})
def update_family_analysed_by(request, family_guid):
"""Updates the specified field in the Family model.
Args:
family_guid (string): GUID of the family.
field_name (string): Family model field name to update
"""
family = Family.objects.get(guid=family_guid)
check_permissions(family.project, request.user, CAN_EDIT)
create_seqr_model(FamilyAnalysedBy, family=family, created_by=request.user)
return create_json_response(
{family.guid: _get_json_for_family(family, request.user)})
def saved_variant_transcripts(request, variant_guid):
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.project, request.user, CAN_VIEW)
# TODO when variant search is rewritten for seqr models use that here
base_project = find_matching_xbrowse_model(saved_variant.project)
loaded_variant = get_datastore(base_project).get_single_variant(
base_project.project_id,
saved_variant.family.family_id,
saved_variant.xpos,
saved_variant.ref,
saved_variant.alt,
)
return create_json_response({variant_guid: {'transcripts': _variant_transcripts(loaded_variant.annotation)}})
def delete_variant_note_handler(request, variant_guid, note_guid):
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.family.project, request.user, CAN_VIEW)
VariantNote.objects.get(guid=note_guid,
saved_variant=saved_variant).delete()
return create_json_response({
'savedVariantsByGuid': {
variant_guid: {
'notes': [
get_json_for_variant_note(tag)
for tag in saved_variant.variantnote_set.all()
]
}
}
})
def delete_variant_note_handler(request, variant_guids, note_guid):
variant_guids = variant_guids.split(',')
note = VariantNote.objects.get(guid=note_guid)
projects = {saved_variant.family.project for saved_variant in note.saved_variants.all()}
for project in projects:
check_permissions(project, request.user, CAN_VIEW)
note.delete()
return create_json_response({
'savedVariantsByGuid': {
saved_variant.guid: {'noteGuids': [n.guid for n in saved_variant.variantnote_set.all()]}
for saved_variant in SavedVariant.objects.filter(guid__in=variant_guids)
},
'variantNotesByGuid': {note_guid: None},
})
def update_variant_tags_handler(request, variant_guid):
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.project, request.user, CAN_VIEW)
request_json = json.loads(request.body)
updated_tags = request_json.get('tags', [])
updated_functional_data = request_json.get('functionalData', [])
# Update tags
existing_tag_guids = [tag['tagGuid'] for tag in updated_tags if tag.get('tagGuid')]
for tag in saved_variant.varianttag_set.exclude(guid__in=existing_tag_guids):
delete_seqr_model(tag)
_create_new_tags(saved_variant, request_json, request.user)
# Update functional data
existing_functional_guids = [tag['tagGuid'] for tag in updated_functional_data if tag.get('tagGuid')]
for tag in saved_variant.variantfunctionaldata_set.exclude(guid__in=existing_functional_guids):
delete_seqr_model(tag)
for tag in updated_functional_data:
if tag.get('tagGuid'):
tag_model = VariantFunctionalData.objects.get(
guid=tag.get('tagGuid'),
functional_data_tag=tag.get('name'),
saved_variant=saved_variant
)
update_model_from_json(tag_model, tag, allow_unknown_keys=True)
else:
create_seqr_model(
VariantFunctionalData,
saved_variant=saved_variant,
functional_data_tag=tag.get('name'),
metadata=tag.get('metadata'),
search_hash=request_json.get('searchHash'),
created_by=request.user,
)
return create_json_response({'savedVariantsByGuid': {
variant_guid: {
'tags': [get_json_for_variant_tag(tag) for tag in saved_variant.varianttag_set.all()],
'functionalData': [get_json_for_variant_functional_data(tag) for tag in saved_variant.variantfunctionaldata_set.all()]
}
}})
def update_family_analysed_by(request, family_guid):
"""Updates the specified field in the Family model.
Args:
family_guid (string): GUID of the family.
field_name (string): Family model field name to update
"""
family = Family.objects.get(guid=family_guid)
# analysed_by can be edited by anyone with access to the project
check_permissions(family.project, request.user, CAN_VIEW)
FamilyAnalysedBy.objects.create(family=family, created_by=request.user)
return create_json_response(
{family.guid: _get_json_for_family(family, request.user)})
def update_family_analysed_by(request, family_guid):
"""Updates the specified field in the Family model.
Args:
family_guid (string): GUID of the family.
field_name (string): Family model field name to update
"""
family = Family.objects.get(guid=family_guid)
check_permissions(family.project, request.user, CAN_EDIT)
create_seqr_model(FamilyAnalysedBy, family=family, created_by=request.user)
return create_json_response({
family.guid: _get_json_for_family(family, request.user)
})
def update_project_categories_handler(request, project_guid):
"""Update ProjectCategories for the given project.
Args:
project_guid (string): GUID of the project that should be updated
HTTP POST
Request body - should contain the following json structure:
{
'form' : {
'categories': a list of category GUIDs for the categories assigned to the given project
}
}
Response body - will contain the following structure, representing the updated project,
as well all categories in seqr:
{
'projectsByGuid': {
<projectGuid1> : { ... <project key-value pairs> ... }
}
'projectCategoriesByGuid': {
<projectCategoryGuid1> : { ... <category key-value pairs> ... }
<projectCategoryGuid2> : { ... <category key-value pairs> ... }
}
}
"""
project = Project.objects.get(guid=project_guid)
# check permissions
check_permissions(project, request.user, CAN_EDIT)
request_json = json.loads(request.body)
# project categories according to the UI
current_category_guids = set(request_json['categories'])
project_categories_by_guid = _update_project_categories(project, request.user, current_category_guids)
projects_by_guid = {
project.guid: _get_json_for_project(project, request.user)
}
return create_json_response({
'projectsByGuid': projects_by_guid,
'projectCategoriesByGuid': project_categories_by_guid,
})
def update_mme_result_status(request, matchmaker_result_guid):
"""
Looks for matches for the given individual. Expects a single patient (MME spec) in the POST
data field under key "patient_data"
Args:
project_id,indiv_id and POST all data in POST under key "patient_data"
Returns:
Status code and results
"""
result = MatchmakerResult.objects.get(guid=matchmaker_result_guid)
project = result.individual.family.project
check_permissions(project, request.user)
request_json = json.loads(request.body)
update_model_from_json(result, request_json, allow_unknown_keys=True)
return create_json_response({
'mmeResultsByGuid': {matchmaker_result_guid: {'matchStatus': _get_json_for_model(result)}},
})
def update_family_fields_handler(request, family_guid):
"""Updates the specified field in the Family model.
Args:
family_guid (string): GUID of the family.
"""
family = Family.objects.get(guid=family_guid)
# check permission
project = family.project
check_permissions(project, request.user, CAN_EDIT)
request_json = json.loads(request.body)
update_family_from_json(family, request_json, user=request.user, allow_unknown_keys=True)
return create_json_response({
family.guid: _get_json_for_family(family, request.user)
})
def _get_project_details(project, user):
check_permissions(project, user)
project_json = _get_json_for_project(project, user)
families_by_guid, individuals_by_guid, samples_by_guid, analysis_groups_by_guid, locus_lists_by_guid = get_project_child_entities(project, user)
project_json.update({
'hasGeneSearch': True,
'locusListGuids': locus_lists_by_guid.keys(),
'variantTagTypes': get_project_variant_tag_types(project),
'variantFunctionalTagTypes': get_json_for_variant_functional_data_tag_types(),
})
return {
'projectsByGuid': {project.guid: project_json},
'familiesByGuid': families_by_guid,
'individualsByGuid': individuals_by_guid,
'samplesByGuid': samples_by_guid,
'locusListsByGuid': locus_lists_by_guid,
'analysisGroupsByGuid': analysis_groups_by_guid,
}
def _phenotips_view_handler(request, project_guid, individual_guid, url_template, permission_level=CAN_VIEW):
"""Requests the PhenoTips PDF for the given patient_id, and forwards PhenoTips' response to the client.
Args:
request: Django HTTP request object
project_guid (string): project GUID for the seqr project containing this individual
individual_guid (string): individual GUID for the seqr individual corresponding to the desired patient
"""
project = Project.objects.get(guid=project_guid)
check_permissions(project, request.user, CAN_VIEW)
individual = Individual.objects.get(guid=individual_guid)
_create_patient_if_missing(project, individual)
_set_phenotips_patient_id_if_missing(project, individual)
# query string forwarding needed for PedigreeEditor button
query_string = request.META["QUERY_STRING"]
url = url_template.format(patient_id=individual.phenotips_patient_id, query_string=query_string)
auth_tuple = _get_phenotips_username_and_password(request.user, project, permissions_level=permission_level)
return proxy_request(request, url, headers={}, auth_tuple=auth_tuple, host=settings.PHENOTIPS_SERVER)
def update_project_handler(request, project_guid):
"""Update project metadata - including one or more of these fields: name, description
Args:
project_guid (string): GUID of the project that should be updated
HTTP POST
Request body - should contain the following json structure:
{
'form' : {
'name': <project name>,
'description': <project description>,
}
}
Response body - will contain the following structure, representing the updated project:
{
'projectsByGuid': {
<projectGuid1> : { ... <project key-value pairs> ... }
}
}
"""
project = Project.objects.get(guid=project_guid)
check_permissions(project, request.user, CAN_EDIT)
request_json = json.loads(request.body)
update_project_from_json(project, request_json, allow_unknown_keys=True)
return create_json_response({
'projectsByGuid': {
project.guid: _get_json_for_project(project, request.user)
},
})
def update_mme_submission(request, individual_guid):
"""
Create or update the submission for the given individual.
"""
individual = Individual.objects.get(guid=individual_guid)
project = individual.family.project
check_permissions(project, request.user)
submission_json = json.loads(request.body)
submission_json.pop('individualGuid', {})
phenotypes = submission_json.pop('phenotypes', [])
gene_variants = submission_json.pop('geneVariants', [])
if not phenotypes and not gene_variants:
return create_json_response({}, status=400, reason='Genotypes or phentoypes are required')
if not submission_json.get('patient', {}).get('id'):
return create_json_response({}, status=400, reason='Patient id is required')
genomic_features = []
for gene_variant in gene_variants:
if not gene_variant.get('geneId'):
return create_json_response({}, status=400, reason='Gene id is required for genomic features')
feature = {'gene': {'id': gene_variant['geneId']}}
if 'numAlt' in gene_variant:
feature['zygosity'] = gene_variant['numAlt'] % 2
if gene_variant.get('pos'):
feature['variant'] = {
'alternateBases': gene_variant['alt'],
'referenceBases': gene_variant['ref'],
'referenceName': gene_variant['chrom'],
'start': gene_variant['pos'],
'assembly': gene_variant['genomeVersion'],
}
genomic_features.append(feature)
submission_json['patient']['genomicFeatures'] = genomic_features
submission_json['patient']['features'] = phenotypes
response = requests.post(url=MME_ADD_INDIVIDUAL_URL, headers=MME_HEADERS, data=json.dumps(submission_json))
if response.status_code not in (200, 409):
try:
response_json = response.json()
except Exception:
response_json = {}
return create_json_response(response_json, status=response.status_code, reason=response.content)
submitted_date = datetime.now()
individual.mme_submitted_data = submission_json
individual.mme_submitted_date = submitted_date
individual.mme_deleted_date = None
individual.mme_deleted_by = None
individual.save()
# update the project contact information if anything new was added
new_contact_names = set(submission_json['patient']['contact']['name'].split(',')) - set(project.mme_primary_data_owner.split(','))
new_contact_urls = set(submission_json['patient']['contact']['href'].replace('mailto:', '').split(',')) - set(project.mme_contact_url.replace('mailto:', '').split(','))
updates = {}
if new_contact_names:
updates['mme_primary_data_owner'] = '{},{}'.format(project.mme_primary_data_owner, ','.join(new_contact_names))
if new_contact_urls:
updates['mme_contact_url'] = '{},{}'.format(project.mme_contact_url, ','.join(new_contact_urls))
if updates:
update_seqr_model(project, **updates)
# search for new matches
return _search_individual_matches(individual, request.user)
def _check_results_permission(results_model, user):
families = results_model.families.prefetch_related('project').all()
projects = {family.project for family in families}
for project in projects:
check_permissions(project, user)