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Merge pull request #181 from IFB-ElixirFr/156-dynamic-bioschemas-prof…
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…ile-generation

Big update on Bioschemas validation (dct:conformsTo)
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@albangaignard
albangaignard authored Mar 2, 2023
2 parents eb5d3a6 + 4bdb370 commit fde869e
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Showing 30 changed files with 116,432 additions and 76,887 deletions.
3 changes: 3 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -15,3 +15,6 @@ notebooks/.ipynb_checkpoints
.vscode
/docs/_build
*.log
metadata_dump/
notebooks/output_dir/
output_dir/
240 changes: 182 additions & 58 deletions app.py
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Original file line number Diff line number Diff line change
Expand Up @@ -58,8 +58,19 @@
from profiles.bioschemas_shape_gen import validate_any_from_microdata
from metrics.util import SOURCE
from metrics.F1B_Impl import F1B_Impl
from metrics.F1B_Impl import F1B_Impl
from urllib.parse import urlparse

from profiles.Profile import Profile
from profiles.ProfileFactory import (
ProfileFactory,
find_conformsto_subkg,
load_profiles,
update_profiles,
evaluate_profile_with_conformsto,
evaluate_profile_from_type,
dyn_evaluate_profile_with_conformsto,
)

import time
import atexit
Expand Down Expand Up @@ -126,6 +137,9 @@ def index():

# Prevent DEV logger from output
dev_logger.propagate = False

# Update bioschemas profile when starting server in production
# update_profiles()
else:
app.config.from_object("config.DevelopmentConfig")

Expand Down Expand Up @@ -213,6 +227,8 @@ def index():
{"name": "a2", "category": "A"},
]

# Load bs profils dict (from github if not already in local)
load_profiles()

METRICS = {}
# json_metrics = test_metric.getMetrics()
Expand Down Expand Up @@ -307,6 +323,8 @@ def display_vocab_status():
scheduler.add_job(
func=F1B_Impl.update_identifiers_org_dump, trigger="interval", seconds=604800
)
scheduler.add_job(func=update_profiles, trigger="interval", seconds=604800)

scheduler.start()

# Shut down the scheduler when exiting the app
Expand Down Expand Up @@ -471,10 +489,16 @@ def get(self):

web_res = WebResource(url)

results = []
for key in METRICS_CUSTOM.keys():
metric = METRICS_CUSTOM[key]
metrics_collection = []
for metric_key in METRICS_CUSTOM.keys():
metric = METRICS_CUSTOM[metric_key]
metric.set_web_resource(web_res)
metrics_collection.append(metric)

# metrics_collection = FAIRMetricsFactory.get_FC_impl(web_res)

results = []
for metric in metrics_collection:
result = metric.evaluate()
data = {
"metric": result.get_metrics(),
Expand Down Expand Up @@ -610,6 +634,7 @@ def get(self):
return check_kg(kg, True)


# TODO update method
@fc_inspect_namespace.route("/bioschemas_validation")
class InspectBioschemas(Resource):
@fc_inspect_namespace.expect(reqparse)
Expand All @@ -620,10 +645,64 @@ def get(self):

web_res = WebResource(url)
kg = web_res.get_rdf()
results = validate_any_from_KG(kg)
results = {}

# Evaluate only profile with conformsTo
results_conformsto = dyn_evaluate_profile_with_conformsto(kg)

# Try to match and evaluate all found corresponding profiles
results_type = evaluate_profile_from_type(kg)

for result_key in results_conformsto.keys():
results[result_key] = results_conformsto[result_key]

for result_key in results_type.keys():
if result_key not in results:
results[result_key] = results_type[result_key]

# TODO Try similarity match her for profiles that are not matched

return results


@fc_inspect_namespace.route("/bioschemas_validation_by_conformsto")
class InspectBioschemasConformsTo(Resource):
@fc_inspect_namespace.expect(reqparse)
def get(self):
"""Validate an RDF JSON-LD graph against Bioschemas profiles using dct:conformsTo"""
args = reqparse.parse_args()
url = args["url"]

web_res = WebResource(url)
kg = web_res.get_rdf()

# Evaluate only profile with conformsTo
results_conformsto = dyn_evaluate_profile_with_conformsto(kg)

# TODO Try similarity match her for profiles that are not matched

return results_conformsto


@fc_inspect_namespace.route("/bioschemas_validation_by_types")
class InspectBioschemasTypesMatch(Resource):
@fc_inspect_namespace.expect(reqparse)
def get(self):
"""Validate an RDF JSON-LD graph against Bioschemas profiles using types"""
args = reqparse.parse_args()
url = args["url"]

web_res = WebResource(url)
kg = web_res.get_rdf()

# Try to match and evaluate all found corresponding profiles
results_type = evaluate_profile_from_type(kg)

# TODO Try similarity match her for profiles that are not matched

return results_type


def list_routes():
return ["%s" % rule for rule in app.url_map.iter_rules()]

Expand Down Expand Up @@ -1522,6 +1601,49 @@ def check_kg_shape(data):
# print(results)


@DeprecationWarning
@socketio.on("check_kg_shape_old")
def check_kg_shape_old(data):
print("shape validation started")
sid = request.sid
print(sid)
kg = KGS[sid]

if not kg:
print("cannot access current knowledge graph")
elif len(kg) == 0:
print("cannot validate an empty knowledge graph")

results = validate_any_from_KG(kg)
emit("done_check_shape", results)


def evaluate_bioschemas_profiles(kg):
# A instancier au lancement du serveur et actualiser lors d'updates
# profiles = ProfileFactory.create_all_profiles_from_specifications()

results = {}

# Evaluate only profile with conformsTo
results_conformsto = dyn_evaluate_profile_with_conformsto(kg)

# Try to match and evaluate all found corresponding profiles
results_type = evaluate_profile_from_type(kg)

for result_key in results_conformsto.keys():
results[result_key] = results_conformsto[result_key]

for result_key in results_type.keys():
if result_key not in results:
results[result_key] = results_type[result_key]

# TODO Try similarity match her for profiles that are not matched

print(results.keys())

return results


@socketio.on("check_kg_shape_2")
def check_kg_shape_2(data):
print("shape validation started")
Expand All @@ -1534,10 +1656,57 @@ def check_kg_shape_2(data):
elif len(kg) == 0:
print("cannot validate an empty knowledge graph")

results = validate_any_from_KG(kg)
results = evaluate_bioschemas_profiles(kg)

# results = validate_any_from_KG(kg)

emit("done_check_shape", results)


def update_bioschemas_valid(func):
@functools.wraps(func)
def wrapper_decorator(*args, **kwargs):
# Do something before
start_time = time.time()

value = func(*args, **kwargs)

# Do something after
elapsed_time = round((time.time() - start_time), 2)
logging.info(f"Bioschemas validation processed in {elapsed_time} s")
# emit("done_check_shape", res, namespace="/validate_bioschemas")
# socketio.emit("done_check_shape", res, namespace="/inspect")
return value

return wrapper_decorator


@app.route("/bioschemas_validation")
@update_bioschemas_valid
def validate_bioschemas():
uri = request.args.get("url")
logging.info(f"Validating Bioschemas markup for {uri}")

kg = WebResource(uri).get_rdf()
print(len(kg))

results = evaluate_bioschemas_profiles(kg)

# res, kg = validate_any_from_microdata(input_url=uri)

m = []
return render_template(
"bioschemas.html",
results=results,
kg=kg,
f_metrics=m,
sample_data=sample_resources,
title="Inspect",
subtitle="to enhance metadata quality",
jld=buildJSONLD(),
)


#######################################
#######################################

Expand Down Expand Up @@ -1707,45 +1876,6 @@ def base_metrics():
# return response


def update_bioschemas_valid(func):
@functools.wraps(func)
def wrapper_decorator(*args, **kwargs):
# Do something before
start_time = time.time()

value = func(*args, **kwargs)

# Do something after
elapsed_time = round((time.time() - start_time), 2)
logging.info(f"Bioschemas validation processed in {elapsed_time} s")
# emit("done_check_shape", res, namespace="/validate_bioschemas")
# socketio.emit("done_check_shape", res, namespace="/inspect")
return value

return wrapper_decorator


@app.route("/validate_bioschemas")
@update_bioschemas_valid
def validate_bioschemas():
uri = request.args.get("uri")
logging.debug(f"Validating Bioschemas markup fr {uri}")

res, kg = validate_any_from_microdata(input_url=uri)

m = []
return render_template(
"bioschemas.html",
results=res,
kg=kg,
f_metrics=m,
sample_data=sample_resources,
title="Inspect",
subtitle="to enhance metadata quality",
jld=buildJSONLD(),
)


@app.route("/inspect")
def kg_metrics_2():
# m = [{ "name": "i1",
Expand Down Expand Up @@ -1867,6 +1997,10 @@ def get_result_style(result) -> str:
sys.exit(1)

args = parser.parse_args()
print(args)

if args.update:
print("UPDATE BS her")

if args.debug:
logging.basicConfig(
Expand Down Expand Up @@ -1901,20 +2035,10 @@ def get_result_style(result) -> str:
web_res = WebResource(url)

metrics_collection = []
metrics_collection.append(FAIRMetricsFactory.get_F1A(web_res))
metrics_collection.append(FAIRMetricsFactory.get_F1B(web_res))
metrics_collection.append(FAIRMetricsFactory.get_F2A(web_res))
metrics_collection.append(FAIRMetricsFactory.get_F2B(web_res))
metrics_collection.append(FAIRMetricsFactory.get_I1(web_res))
metrics_collection.append(FAIRMetricsFactory.get_I1A(web_res))
metrics_collection.append(FAIRMetricsFactory.get_I1B(web_res))
metrics_collection.append(FAIRMetricsFactory.get_I2(web_res))
metrics_collection.append(FAIRMetricsFactory.get_I2A(web_res))
metrics_collection.append(FAIRMetricsFactory.get_I2B(web_res))
metrics_collection.append(FAIRMetricsFactory.get_I3(web_res))
metrics_collection.append(FAIRMetricsFactory.get_R11(web_res))
metrics_collection.append(FAIRMetricsFactory.get_R12(web_res))
metrics_collection.append(FAIRMetricsFactory.get_R13(web_res))
for metric_key in METRICS_CUSTOM.keys():
metric = METRICS_CUSTOM[metric_key]
metric.set_web_resource(web_res)
metrics_collection.append(metric)

if args.bioschemas:
logging.info("Bioschemas eval")
Expand Down
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