Adding date back, change dashboard score function

- add date updated back to ontology pages
- Make sure that the dashboard score is shown on ontology pages
- Show link back to overview pages
- Add new function for a simpler dashboard score, see #64
- refactor URL exists check

util/dashboard/dashboard.py

@@ -29,7 +29,7 @@
 
 from argparse import ArgumentParser, FileType
 from py4j.java_gateway import JavaGateway
-from lib import round_float, compute_dashboard_score, compute_obo_score, DashboardConfig, \
+from lib import round_float, compute_dashboard_score_alt1, compute_obo_score, DashboardConfig, \
     create_dashboard_score_badge, create_dashboard_qc_badge
 
 
@@ -367,7 +367,7 @@ def run():
         summary_count['WARN'] = warn
         summary_count['INFO'] = info
         date = datetime.datetime.today()
-        save_data = {'namespace': namespace, 'version': version_iri,
+        save_data = {'namespace': namespace, 'version': version_iri, 'date': date,
                      'summary': {'status': summary, 'comment': summary_comment, 'summary_count': summary_count}, 'results': all_checks}
 
         oboscore_weights = config.get_oboscore_weights()
@@ -376,8 +376,9 @@ def run():
         for key in save_data:
             data_yml[key] = save_data[key]
 
-        obo_dashboard_score = round_float(
-            float(compute_dashboard_score(data_yml, oboscore_weights, oboscore_maximpacts)) / 100)
+        raw_dashboard_score = compute_dashboard_score_alt1(data_yml, oboscore_weights, oboscore_maximpacts)
+        raw_dashboard_score = float(raw_dashboard_score) / float(100)
+        obo_dashboard_score = round_float(float(raw_dashboard_score))
         data_yml['metrics']['Info: Experimental OBO score']['_dashboard'] = obo_dashboard_score
         oboscore = compute_obo_score(data_yml['metrics']['Info: Experimental OBO score']['_impact'],
                                      data_yml['metrics']['Info: Experimental OBO score']['_reuse'],
@@ -388,12 +389,11 @@ def run():
         data_yml['metrics']['Info: Experimental OBO score']['oboscore'] = round_float(oboscore['score'])
         data_yml['metrics']['Info: Experimental OBO score']['_formula'] = oboscore['formula']
 
-
-
+        obo_dashboard_score_pc = round_float(float((obo_dashboard_score*100)))
         # Save to YAML file
         print('Saving results to {0}'.format(dashboard_yml))
         create_dashboard_qc_badge(color, ", ".join(badge_message), ontology_dir)
-        create_dashboard_score_badge("blue", obo_dashboard_score, ontology_dir)
+        create_dashboard_score_badge("blue", f"{obo_dashboard_score_pc} %", ontology_dir)
 
         with open(dashboard_yml, 'w+') as f:
             yaml.dump(data_yml, f)

util/dashboard/fp_004.py

@@ -24,6 +24,7 @@
 
 import dash_utils
 import re
+from lib import url_exists
 
 import requests
 
@@ -99,16 +100,3 @@ def big_has_versioning(file):
 
     return {'status': 'PASS'}
 
-
-def url_exists(url: str) -> bool:
-    # check the URL resolves, but don't download it in full
-    # inspired by https://stackoverflow.com/a/61404519/5775947
-    try:
-        with requests.get(url, stream=True) as res:
-            rv = res.status_code == 200
-    except Exception:
-        # Any errors with connection will be considered
-        # as the URL not existing
-        return False
-    else:
-        return rv

util/dashboard/fp_008.py

@@ -28,8 +28,8 @@
 ## ### Implementation
 ## The registry data is checked for 'homepage' and 'description' entries. If either is missing, this is an error. If the homepage is present, the URL is checked to see if it resolves (does not return an HTTP status of greater than 400). If the URL does not resolve, this is also an error.
 
-import requests
 
+from lib import url_exists
 
 def has_documentation(data):
     """Check fp 8 - documentation.
@@ -64,12 +64,8 @@ def has_documentation(data):
                 'comment': 'Missing description'}
 
     # check if URL resolves
-    try:
-        request = requests.get(home)
-    except Exception as e:
+    if not url_exists(home):
         return {'status': 'ERROR',
-                'comment': 'homepage URL ({0}) does not resolve'.format(home)}
-    if request.status_code > 400:
-        return {'status': 'ERROR',
-                'comment': 'homepage URL ({0}) does not resolve'.format(home)}
+                'comment': 'Homepage URL ({0}) does not resolve'.format(home)}
+
     return {'status': 'PASS'}

util/dashboard_config.py

@@ -450,7 +450,10 @@ def prepare_ontologies(ontologies, ontology_dir, dashboard_dir, make_parameters,
                     # Only overwrite these metrics when we actually overwrite the dashboard..
                     ont_results['metrics']['Info: Which ontologies use it?'] = [use for use in uses if use != o]
                     ont_results['metrics']['Info: How many ontologies use it?'] = uses_count
-                    ont_results['metrics']['Info: Experimental OBO score'] = dashboard_score
+                    if 'Info: Experimental OBO score' in ont_results['metrics']:
+                        ont_results['metrics']['Info: Experimental OBO score'].update(dashboard_score)
+                    else:
+                        ont_results['metrics']['Info: Experimental OBO score'] = dashboard_score
                     save_yaml(ont_results, ont_results_path)
                     runcmd(f"make  {make_parameters} {dashboard_html}", config.get_dashboard_report_timeout_seconds())
                     ont_results.pop('last_ontology_dashboard_run_failed', None)

util/lib.py

@@ -452,6 +452,44 @@ def compute_dashboard_score(data, weights, maximpacts):
     oboscore = oboscore - score_max(weights['report_info'] * report_info, maximpacts['report_info'])
     return "%.2f" % oboscore
 
+def compute_dashboard_score_alt1(data, weights, maximpacts):
+    """Computing dashboard score based purely on the number of failed categories"""
+
+    if 'failure' in data:
+        return 0
+
+    score = 100
+
+    if 'results' in data:
+        ct_categories = len(data['results']) + 1 # The + 1 is the requirement of having a base.
+        weight_per_category = float((100 / ct_categories))
+        for cat in data['results']:
+            if 'status' in data['results'][cat]:
+                if data['results'][cat]['status'] == 'ERROR':
+                    score -= weight_per_category
+                elif data['results'][cat]['status'] == 'WARN':
+                    score -= (weight_per_category/3)
+                elif data['results'][cat]['status'] == 'INFO':
+                    score -= (weight_per_category / 10)
+                elif data['results'][cat]['status'] == 'PASS':
+                    score -= 0
+                else:
+                    logging.warning(f"compute_dashboard_score_alt1(): Results section exists but unrecognised status {data['results'][cat]['status']}.")
+                    return 0
+            else:
+                logging.warning(
+                    f"compute_dashboard_score_alt1(): Results section exists but no status entry for {cat}.")
+                return 0
+    else:
+        return 0
+
+    if 'base_generated' in data and data['base_generated'] == True:
+        score -= weight_per_category
+
+    if score < 0:
+        score = 0
+
+    return "%.2f" % score
 
 def round_float(n):
     strfloat = "%.3f" % n
@@ -514,3 +552,15 @@ def create_badge(color: str, message: str, label:str, filepath: str):
     json_string = json.dumps(json_data)
     with open(filepath, "w") as text_file:
         print(json_string, file=text_file)
+
+def url_exists(url: str) -> bool:
+    # check the URL resolves, but don't download it in full
+    # inspired by https://stackoverflow.com/a/61404519/5775947
+    try:
+        with requests.get(url, stream=True) as res:
+            return (res.status_code == 200)
+    except Exception as e:
+        # Any errors with connection will be considered
+        # as the URL not existing
+        logging.error(e, exc_info=True)
+    return False

util/templates/ontology.html.jinja2

@@ -11,6 +11,7 @@
                 <p class="lead"><b>Version</b>: {{ o.version }}</p>
                 <p class="lead" style="margin-top:-15px;"><b>Date run</b>: {{ o.date }}</p>
                 <p class="lead" style="margin-top:-15px;"><a href="dashboard.yml">View dashboard results as YAML</a></p>
+                <p class="lead" style="margin-top:-15px;"><a href="../index.html">Go back to Overview</a></p>
                 <h3>Error Breakdown</h3>
                 {% set summary = o.summary %}
                 {% if 'comment' in summary %}