def test_process_rag_traits(testing_db: RagsProjectDB):
reset_db(testing_db)
project_id = create_project_with_rags(testing_db)
db_project = testing_db.get_project_by_id(project_id)
test_project = RagsProjectManager(db_project.id, db_project.name,
testing_db)
test_project.process_traits()
for study in testing_db.get_all_studies(project_id):
assert study.trait_normalized
def test_get_projects(testing_db: RagsProjectDB):
reset_db(testing_db)
testing_db.create_project('Testing Project')
testing_db.create_project('Testing Project 2')
testing_db.create_project('Testing Project 3')
projects = testing_db.get_projects()
assert len(projects) == 3
for p in projects:
assert type(p) == rags_db_models.RAGsProject
assert 'Test' in p.name
def build_rags(request: Request,
project_id: int = Form(...),
force_rebuild: bool = Form(...),
rags_project_db: RagsProjectDB = Depends(get_db)):
template_context = init_template_context(request)
db_project = rags_project_db.get_project_by_id(project_id)
project_manager = RagsProjectManager(db_project.id, db_project.name,
rags_project_db)
try:
results = project_manager.process_traits(force_rebuild=force_rebuild)
update_template_context_with_results(results, template_context)
if not results.success:
return templates.TemplateResponse("error.html.jinja",
template_context)
results = project_manager.search_studies()
update_template_context_with_results(results, template_context)
results = project_manager.build_rags(force_rebuild=force_rebuild)
update_template_context_with_results(results, template_context)
if not results.success:
return templates.TemplateResponse("error.html.jinja",
template_context)
except RagsGraphDBConnectionError:
show_graph_db_connection_error(template_context)
return templates.TemplateResponse("error.html.jinja", template_context)
except RagsNormalizationError as e:
show_error_message(template_context, e.message)
return templates.TemplateResponse("error.html.jinja", template_context)
return get_manage_project_view_template(rags_project_db, project_id,
template_context)
def get_project_query_view(rags_project_db: RagsProjectDB, project_id: int,
template_context: dict):
project = rags_project_db.get_project_by_id(project_id)
template_context["project"] = project
return templates.TemplateResponse("project_queries.html.jinja",
template_context)
def delete_study(request: Request,
study_id: int = Form(...),
rags_project_db: RagsProjectDB = Depends(get_db)):
template_context = init_template_context(request)
study = rags_project_db.get_study_by_id(study_id)
if study and rags_project_db.delete_study(study):
study_name = study.study_name
show_success_message(
template_context,
f"Association study {study_name} was deleted successfully.")
else:
show_error_message(
template_context,
"That association study doesn't exist or was already deleted.")
return get_manage_project_view_template(rags_project_db, study.project_id,
template_context)
def add_study(request: Request,
project_id: int = Form(...),
study_name: str = Form(...),
study_type: str = Form(...),
trait_id: str = Form(...),
trait_type: str = Form(...),
trait_label: str = Form(...),
p_value_threshold: float = Form(...),
max_p_value: float = Form(...),
file_path: str = Form(...),
has_tabix: bool = Form(False),
rags_project_db: RagsProjectDB = Depends(get_db)):
template_context = init_template_context(request)
if not rags_project_db.project_exists_by_id(project_id):
return get_missing_project_view_template(template_context)
if rags_project_db.study_exists(project_id, study_name):
show_warning_message(
template_context,
f'An association study with that name ({study_name}) already exists in this project.'
)
return get_manage_project_view_template(rags_project_db, project_id,
template_context)
if rags_project_db.create_study(project_id=project_id,
study_name=study_name,
study_type=study_type,
original_trait_id=trait_id,
original_trait_type=trait_type,
original_trait_label=trait_label,
p_value_cutoff=p_value_threshold,
max_p_value=max_p_value,
file_path=file_path,
has_tabix=has_tabix):
show_success_message(
template_context,
f'A new association study was added. ({study_name})')
show_warning_message(
template_context,
'Continue to "Build Graph" when you are done adding studies!')
else:
show_error_message(template_context, f'Error creating ({study_name}).')
return get_manage_project_view_template(rags_project_db, project_id,
template_context)
def test_project_deletion(testing_db: RagsProjectDB):
reset_db(testing_db)
testing_db.create_project('Testing Project')
new_project_id = testing_db.get_project_by_name('Testing Project').id
testing_db.delete_project(new_project_id)
assert testing_db.project_exists_by_id(new_project_id) is False
assert testing_db.get_project_by_name('Testing Project') is None
def test_create_rags(testing_db: RagsProjectDB):
reset_db(testing_db)
project_id = create_project_with_rags(testing_db)
assert len(testing_db.get_all_studies(project_id)) == 5
assert testing_db.study_exists(project_id, 'Testing GWAS 1')
assert testing_db.study_exists(project_id, 'Testing GWAS 2')
assert testing_db.study_exists(project_id, 'Testing GWAS 3')
assert testing_db.study_exists(project_id, 'Testing GWAS 4')
r = testing_db.get_study_by_name('Testing GWAS 1')
assert r.study_type == GWAS
assert r.file_path == f'sample_sugen.gz'
assert r.p_value_cutoff == 0.005
assert r.original_trait_id == 'MONDO:0011122'
assert r.original_trait_type == DISEASE
assert r.original_trait_label == 'Obesity'
assert not r.searched
assert not r.written
def get_manage_project_view_template(rags_project_db: RagsProjectDB,
project_id: int, template_context: dict):
project = rags_project_db.get_project_by_id(project_id)
template_context["project"] = project
template_context["studies"] = project.studies
template_context["study_type_list"] = RAGS_STUDY_TYPES
template_context["trait_type_list"] = RAGS_TRAIT_TYPES
return templates.TemplateResponse("project_management.html.jinja",
template_context)
def manage_project(project_id: int,
request: Request,
rags_project_db: RagsProjectDB = Depends(get_db)):
template_context = init_template_context(request)
if not rags_project_db.project_exists_by_id(project_id):
return get_missing_project_view_template(template_context)
return get_manage_project_view_template(rags_project_db, project_id,
template_context)
def add_project(request: Request,
new_project_name: str = Form(...),
rags_project_db: RagsProjectDB = Depends(get_db)):
template_context = init_template_context(request)
if rags_project_db.project_exists_by_name(new_project_name):
show_error_message(
template_context,
f'A project with that name already exists. ({new_project_name})')
else:
if rags_project_db.create_project(new_project_name):
show_success_message(
template_context,
f'A new project was added. ({new_project_name})')
else:
show_error_message(template_context,
f'Error adding project. ({new_project_name})')
set_up_projects_for_display(template_context, rags_project_db)
return templates.TemplateResponse("projects.html.jinja", template_context)
def test_search_rags(testing_db: RagsProjectDB):
reset_db(testing_db)
project_id = create_project_with_rags(testing_db)
db_project = testing_db.get_project_by_id(project_id)
test_project = RagsProjectManager(db_project.id, db_project.name,
testing_db)
test_project.search_studies()
for r in testing_db.get_all_studies(project_id):
assert r.searched
if r.study_name == 'Testing GWAS 1':
assert r.num_hits == 0
elif r.study_name == 'Testing GWAS 2':
assert r.num_hits == 1
elif r.study_name == 'Testing GWAS 3':
assert r.num_hits == 7
hits = testing_db.get_all_gwas_hits(project_id)
assert len(hits) == 8
for h in hits:
assert not h.written
def project_query_view(project_id: int,
request: Request,
rags_project_db: RagsProjectDB = Depends(get_db)):
template_context = init_template_context(request)
if not rags_project_db.project_exists_by_id(project_id):
show_error_message(
template_context,
"Oh No. That project seems to be missing from the database.")
return templates.TemplateResponse("error.html.jinja", template_context)
return get_project_query_view(rags_project_db, project_id,
template_context)
def delete_project(request: Request,
project_id: int = Form(...),
rags_project_db: RagsProjectDB = Depends(get_db)):
template_context = init_template_context(request)
if not rags_project_db.project_exists_by_id(project_id):
error_message = "That project doesn't exist or was already deleted."
show_error_message(template_context, error_message)
return templates.TemplateResponse("error.html.jinja", template_context)
try:
rags_graph_db = RagsGraphDB()
rags_graph_db.delete_project(project_id)
except RagsGraphDBConnectionError:
show_graph_db_connection_error(template_context)
return templates.TemplateResponse("error.html.jinja", template_context)
rags_project_db.delete_project(project_id)
show_success_message(template_context, f'Project deleted successfully.')
set_up_projects_for_display(template_context, rags_project_db)
return templates.TemplateResponse("projects.html.jinja", template_context)
def a_test_build_rags(testing_db: RagsProjectDB):
reset_db(testing_db)
project_id = create_project_with_rags(testing_db)
db_project = testing_db.get_project_by_id(project_id)
test_project = RagsProjectManager(db_project.id, db_project.name,
testing_db)
result = test_project.process_traits()
assert result.success
result = test_project.search_studies()
assert result.success
result = test_project.build_rags()
assert result.success
rags = testing_db.get_all_studies(project_id)
for r in rags:
assert r.searched
assert r.written
hits = testing_db.get_unprocessed_gwas_hits(project_id)
assert len(hits) == 0
def annotate_rags(request: Request,
project_id: int = Form(...),
rags_project_db: RagsProjectDB = Depends(get_db)):
template_context = init_template_context(request)
db_project = rags_project_db.get_project_by_id(project_id)
project_manager = RagsProjectManager(db_project.id, db_project.name,
rags_project_db)
try:
results = project_manager.annotate_hits()
update_template_context_with_results(results, template_context)
except RagsGraphDBConnectionError:
show_graph_db_connection_error(template_context)
return templates.TemplateResponse("error.html.jinja", template_context)
except RagsNormalizationError as e:
show_error_message(template_context, e.message)
return templates.TemplateResponse("error.html.jinja", template_context)
return get_manage_project_view_template(rags_project_db, project_id,
template_context)
def set_up_projects_for_display(template_context: dict,
rags_project_db: RagsProjectDB):
# here we are dynamically adding some properties jinja expects to the project objects
# this is pretty inefficient, these could be stored in the DB
template_context["projects"] = rags_project_db.get_projects()
for project in template_context["projects"]:
project.num_gwas_files = 0
project.num_gwas_hits = 0
project.num_mwas_files = 0
project.num_mwas_hits = 0
project.num_errors = 0
for study in project.studies:
if study.study_type == GWAS:
project.num_gwas_files += 1
if study.num_hits:
project.num_gwas_hits += study.num_hits
elif study.study_type == MWAS:
project.num_mwas_files += 1
if study.num_hits:
project.num_mwas_hits += study.num_hits
project.num_errors += len(study.errors)
def create_project_with_rags(testing_db: RagsProjectDB):
testing_db.create_project('Testing Project')
project_id = testing_db.get_project_by_name('Testing Project').id
testing_db.create_study(project_id=project_id,
file_path=f'sample_sugen.gz',
study_name="Testing GWAS 1",
study_type=GWAS,
original_trait_id='MONDO:0011122',
original_trait_type=DISEASE,
original_trait_label='Obesity',
p_value_cutoff=0.005,
max_p_value=1,
has_tabix=True)
testing_db.create_study(project_id=project_id,
file_path=f'sample_sugen2.gz',
study_name="Testing GWAS 2",
study_type=GWAS,
original_trait_id='MONDO:0011122',
original_trait_type=DISEASE,
original_trait_label='Obesity',
p_value_cutoff=0.005,
max_p_value=1,
has_tabix=True)
testing_db.create_study(project_id=project_id,
file_path=f'sample_sugen3.gz',
study_name="Testing GWAS 3",
study_type=GWAS,
original_trait_id='MONDO:0011122',
original_trait_type=DISEASE,
original_trait_label='Obesity',
p_value_cutoff=0.005,
max_p_value=1,
has_tabix=True)
testing_db.create_study(project_id=project_id,
file_path=f'sample_sugen4.gz',
study_name="Testing GWAS 4",
study_type=GWAS,
original_trait_id='MONDO:0011122',
original_trait_type=DISEASE,
original_trait_label='Obesity',
p_value_cutoff=0.005,
max_p_value=1,
has_tabix=True)
testing_db.create_study(project_id=project_id,
file_path=f'sample_mwas',
study_name="Testing MWAS",
study_type=MWAS,
original_trait_id='MONDO:0011122',
original_trait_type=DISEASE,
original_trait_label='Obesity',
p_value_cutoff=0.005,
max_p_value=1)
return project_id
def get_db():
try:
db = SessionLocal()
yield RagsProjectDB(db)
finally:
db.close()
def testing_db():
try:
db = TestSessionLocal()
yield RagsProjectDB(db)
finally:
db.close()
def test_delete_rags(testing_db: RagsProjectDB):
reset_db(testing_db)
project_id = create_project_with_rags(testing_db)
for study in testing_db.get_all_studies(project_id):
testing_db.delete_study(study)
assert len(testing_db.get_all_studies(project_id)) == 0
def project_query_view(project_id: int,
query_id: int,
request: Request,
rags_project_db: RagsProjectDB = Depends(get_db)):
template_context = init_template_context(request)
if not rags_project_db.project_exists_by_id(project_id):
show_error_message(
template_context,
f"Oh No. That project seems to be missing from the database.")
return templates.TemplateResponse("error.html.jinja", template_context)
try:
rags_graph_db = RagsGraphDB()
normalized_association_predicate = "biolink:correlated_with"
if query_id == 1:
custom_query = f"match (s:`{SEQUENCE_VARIANT}`)<-[r:`{normalized_association_predicate}` {{project_id: {project_id}}}]-(b) return distinct s.id, r.input_id, r.namespace, b.id, r.p_value ORDER BY r.p_value"
results = rags_graph_db.custom_read_query(custom_query, limit=150)
template_context[
"project_query"] = custom_query + " (limited to 150 results)"
template_context["project_query_results"] = results
template_context["project_query_headers"] = [
"Variant ID", "Original ID", "Association Study",
"Associated with", "p-value"
]
elif query_id == 2:
custom_query = f"match (c:`{CHEMICAL_SUBSTANCE}`)<-[r:`{normalized_association_predicate}` {{project_id: {project_id}}}]-(b) return distinct c.id, r.input_id, r.namespace, b.id, r.p_value ORDER BY r.p_value"
results = rags_graph_db.custom_read_query(custom_query, limit=150)
template_context[
"project_query"] = custom_query + " (limited to 150 results)"
template_context["project_query_results"] = results
template_context["project_query_headers"] = [
"Metabolite ID", "Original ID", "Association Study",
"Associated with", "p-value"
]
elif query_id == 3:
custom_query = f"MATCH (s:`{SEQUENCE_VARIANT}`)<-[r1:`{normalized_association_predicate}` {{project_id: {project_id}}}]-(d:`{DISEASE_OR_PHENOTYPIC_FEATURE}`)-[r2:`{normalized_association_predicate}` {{project_id: {project_id}}}]-(c:`{CHEMICAL_SUBSTANCE}`)-[r3:`{normalized_association_predicate}` {{project_id: {project_id}}}]-(s) return s.id, r1.p_value, d.id, r2.p_value, c.id, r3.p_value ORDER BY r1.p_value"
results = rags_graph_db.custom_read_query(custom_query, limit=150)
template_context[
"project_query"] = custom_query + " (limited to 150 results)"
template_context["project_query_results"] = results
template_context["project_query_headers"] = [
"Variant", "Var-Pheno p-value", "Phenotype",
"Pheno-Chemical p-value", "Chemical", "Chemical-Var p-value"
]
elif query_id == 4:
custom_query = f"MATCH (s:`{SEQUENCE_VARIANT}`)-[r1:`{normalized_association_predicate}` {{project_id: {project_id}}}]-(d:`{DISEASE_OR_PHENOTYPIC_FEATURE}`)-[r2:`{normalized_association_predicate}` {{project_id: {project_id}}}]-(c:`{CHEMICAL_SUBSTANCE}`)-[r3]-(g:gene)-[r4]-(s) WHERE r1.p_value < 1e-5 AND r2.p_value < 1e-5 RETURN s.id, r1.p_value, d.id, r2.p_value, c.id, type(r3), g.id, type(r4)"
results = rags_graph_db.custom_read_query(custom_query, limit=150)
template_context[
"project_query"] = custom_query + " (limited to 150 results)"
template_context["project_query_results"] = results
template_context["project_query_headers"] = [
"Variant", "Var-Pheno p-value", "Phenotype",
"Pheno-Chemical p-value", "Chemical", "Chem-Gene relationship",
"Gene", "Gene-Variant relationship"
]
elif query_id == 5:
pass
except RagsGraphDBConnectionError:
show_graph_db_connection_error(template_context)
return templates.TemplateResponse("error.html.jinja", template_context)
return get_project_query_view(rags_project_db, project_id,
template_context)
def add_studies_by_file(request: Request,
project_id: int = Form(...),
uploaded_studies_file: UploadFile = File(...),
rags_project_db: RagsProjectDB = Depends(get_db)):
template_context = init_template_context(request)
if not rags_project_db.project_exists_by_id(project_id):
return get_missing_project_view_template(template_context)
success = True
try:
dataframe = pd.read_csv(uploaded_studies_file.file, header=0)
for i, row in dataframe.iterrows():
study_name = row["study_name"]
if rags_project_db.study_exists(project_id, study_name):
show_warning_message(
template_context,
f'An association study with the name ({study_name}) already exists.'
)
else:
study_type = row["study_type"]
original_trait_id = row["trait_id"]
original_trait_type = row["trait_type"]
original_trait_label = row["trait_label"]
p_value_cutoff = float(row["p_value_threshold"])
max_p_value = float(
row["max_p_value"]) if "max_p_value" in row else None
file_path = row["file_path"]
has_tabix = True if "has_tabix" in row and row[
"has_tabix"] else False
if not rags_project_db.create_study(
project_id=project_id,
file_path=file_path,
study_name=study_name,
study_type=study_type,
original_trait_id=original_trait_id,
original_trait_type=original_trait_type,
original_trait_label=original_trait_label,
p_value_cutoff=p_value_cutoff,
max_p_value=max_p_value,
has_tabix=has_tabix):
show_error_message(template_context,
f'Error creating {study_name}.')
success = False
except KeyError as k:
error_message = f"Error parsing the association studies file. (KeyError: Key not found {k})"
show_error_message(template_context, error_message)
return templates.TemplateResponse("error.html.jinja", template_context)
except (TypeError, ValueError) as e:
error_message = f"TypeError or ValueError parsing the association studies file. (Error: {e})"
show_error_message(template_context, error_message)
return templates.TemplateResponse("error.html.jinja", template_context)
if success:
show_success_message(
template_context,
"Association studies were added to the project successfully.")
show_warning_message(
template_context,
'Continue to "Build Graph" when you are done adding studies!')
return get_manage_project_view_template(rags_project_db, project_id,
template_context)