Update Automated checks pages (#2656)

* add fp_020.py script to makefile to be updated automatically from OBO-Dashboard

* add fp_20 to be updated automatically; fix bug to have ID

* update checks page auto

---------

Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>

Author: anitacaron

principles/Makefile

@@ -1,7 +1,7 @@
 # Collect the list of query files for report.
 SCRIPTS := build/fp_001.py build/fp_002.py build/fp_003.py build/fp_004.py \
 build/fp_005.py build/fp_006.py build/fp_007.py build/fp_008.py build/fp_009.py \
-build/fp_011.py build/fp_012.py build/fp_016.py 
+build/fp_011.py build/fp_012.py build/fp_016.py build/fp_020.py
 DOCS := $(foreach x, $(SCRIPTS), checks/$(notdir $(basename $(x))).md)
 
 # FP ID to the principle name
@@ -17,6 +17,7 @@ DOCS := $(foreach x, $(SCRIPTS), checks/$(notdir $(basename $(x))).md)
 11 = 'Locus of Authority'
 12 = 'Naming Conventions'
 16 = Maintenance
+20 = Responsiveness
 
 # Generate all check docs
 all: clean
@@ -33,7 +34,7 @@ build/fp_%.py: | build
 
 # Build the MD page from the check script
 checks/fp_%.md: build/fp_%.py | $(SCRIPTS) checks
-	$(eval ID := $(subst 0,,$(subst fp_,,$(notdir $(basename $@)))))
+	$(eval ID := $(shell echo $(subst fp_,,$(notdir $(basename $@))) | sed 's/^0*//'))
 	if [ $(ID) == 1 ]; then export TITLE=$(1); \
 	elif [ $(ID) == 2 ]; then export TITLE=$(2); \
 	elif [ $(ID) == 3 ]; then export TITLE=$(3); \
@@ -46,6 +47,7 @@ checks/fp_%.md: build/fp_%.py | $(SCRIPTS) checks
 	elif [ $(ID) == 11 ]; then export TITLE=$(11); \
 	elif [ $(ID) == 12 ]; then export TITLE=$(12); \
 	elif [ $(ID) == 16 ]; then export TITLE=$(16); \
+	elif [ $(ID) == 20 ]; then export TITLE=$(20); \
 	fi; \
 	echo "---\nlayout: check\nid: $(ID)\ntitle: $$TITLE Automated Check\n---\n" > $@
 	tail -n+3 $< \

principles/checks/fp_001.md

@@ -1,6 +1,6 @@
 ---
 layout: check
-id: fp_001
+id: 1
 title: Open Automated Check
 ---
 
@@ -39,11 +39,11 @@ See [Open Implementation](http://obofoundry.org/principles/fp-001-open.html#impl
 The registry data entry is validated with JSON schema using the [license schema](https://raw.githubusercontent.com/OBOFoundry/OBOFoundry.github.io/master/util/schema/license.json). The license schema ensures that a license entry is present and that the entry has a `url` and `label`. The license schema also checks that the license is one of the CC0 or CC-BY licenses. OWL API is then used to check the ontology as an `OWLOntology` object. Annotations on the ontology are retrieved and the `dcterms:license` property is found. The python script ensures that the correct `dcterms:license` property is used. The script compares this license to the registry license to ensure that they are the same.
 
 ```python
-import jsonschema
 import dash_utils
+import jsonschema
 
 
-def is_open(ontology, data):
+def is_open(ontology, data, schema):
    """Check FP 1 - Open.
 
    This method checks the following:
@@ -63,7 +63,7 @@ def is_open(ontology, data):
        ERROR, WARN, INFO, or PASS string with optional message.
    """
 
-   v = OpenValidator(ontology, data)
+   v = OpenValidator(ontology, data, schema)
 
    loadable = False
    if ontology:
@@ -91,7 +91,7 @@ class OpenValidator():
                                 license (None if missing)
    """
 
-   def __init__(self, ontology, data):
+   def __init__(self, ontology, data, schema):
        """Instantiate an OpenValidator.
 
        Args:
@@ -105,7 +105,7 @@ class OpenValidator():
 
        self.is_open = None
        if self.registry_license is not None:
-           self.is_open = check_registry_license(data)
+           self.is_open = check_registry_license(data, schema)
 
        self.ontology_license = None
        self.correct_property = None
@@ -134,18 +134,18 @@ class OpenValidator():
        annotations = ontology.getAnnotations()
        license = dash_utils.get_ontology_annotation_value(annotations,
                                                           license_prop)
-       bad_license = dash_utils.get_ontology_annotation_value(
-           annotations, bad_license_prop)
+
+       bad_licenses = list(filter(None, [dash_utils.get_ontology_annotation_value(annotations, prop) for prop in bad_license_props]))
 
        if license:
            self.ontology_license = license
            self.correct_property = True
-       elif bad_license:
-           self.ontology_license = bad_license
+       elif len(bad_licenses) > 0:
+           self.ontology_license = bad_licenses[0]
            self.correct_property = False
 
 
-def big_is_open(file, data):
+def big_is_open(file, data, schema):
    """Check FP 1 - Open.
 
    This method checks the following:
@@ -165,7 +165,7 @@ def big_is_open(file, data):
        ERROR, WARN, INFO, or PASS string with optional message.
    """
 
-   v = BigOpenValidator(file, data)
+   v = BigOpenValidator(file, data, schema)
    return process_results(v.registry_license,
                           v.ontology_license,
                           v.is_open,
@@ -188,7 +188,7 @@ class BigOpenValidator():
                                 license (None if missing)
    """
 
-   def __init__(self, file, data):
+   def __init__(self, file, data, schema):
        """Instantiate a BigOpenValidator.
 
        Args:
@@ -202,7 +202,7 @@ class BigOpenValidator():
 
        self.is_open = None
        if self.registry_license is not None:
-           self.is_open = check_registry_license(data)
+           self.is_open = check_registry_license(data, schema)
 
        self.ontology_license = None
        self.correct_property = None
@@ -276,7 +276,7 @@ class BigOpenValidator():
 # ---------- UTILITY METHODS ---------- #
 
 
-def check_registry_license(data):
+def check_registry_license(data, schema):
    """Use the JSON license schema to validate the registry data.
 
    This ensures that the license is present and one of the CC0 or CC-BY
@@ -290,7 +290,7 @@ def check_registry_license(data):
    """
 
    try:
-       jsonschema.validate(data, license_schema)
+       jsonschema.validate(data, schema)
        return True
    except jsonschema.exceptions.ValidationError as ve:
        return False
@@ -304,7 +304,7 @@ def compare_licenses(registry_license, ontology_license):
        ontology_license (str): license URL from the ontology
 
    Return:
-       True if registry license matches ontology licences;
+       True if registry license matches ontology license;
        False if the licenses do not match;
        None if one or both licenses are missing.
    """
@@ -380,7 +380,7 @@ def process_results(registry_license,
        level = 'ERROR'
        issues.append(missing_ontology_license)
 
-   # matches_ontology = None if missing ontology licenese
+   # matches_ontology = None if missing ontology license
    if matches_ontology is False:
        level = 'ERROR'
        issues.append(no_match.format(ontology_license, registry_license))
@@ -395,11 +395,8 @@ def process_results(registry_license,
    return {'status': level, 'comment': ' '.join(issues)}
 
 
-# correct dc license property namespace
+# correct dc license property
 license_prop = 'http://purl.org/dc/terms/license'
-# incorrect dc license property namespace
-bad_license_prop = 'http://purl.org/dc/elements/1.1/license'
-
-# license JSON schema for registry validation
-license_schema = dash_utils.load_schema('dependencies/license.json')
+# incorrect dc license properties
+bad_license_props = ['http://purl.org/dc/elements/1.1/license', 'http://purl.org/dc/elements/1.1/rights', 'http://purl.org/dc/terms/rights']
 ```

principles/checks/fp_002.md

@@ -25,36 +25,19 @@ import dash_utils
 from dash_utils import format_msg
 
 
-def is_common_format(ontology):
+def is_common_format(syntax):
    """Check FP 2 - Common Format.
 
    Args:
-       ontology (OWLOntology): ontology object
+       syntax (str): the syntax as determined by ROBOT metrics
 
    Return:
        PASS if OWLOntology is not None, ERROR otherwise.
    """
-   if ontology is None:
-       return {'status': 'ERROR', 'comment': 'Unable to load ontology'}
-   else:
+   if syntax is None:
+       return {'status': 'ERROR', 'comment': 'Unknown format'}
+   elif syntax == "RDF/XML Syntax":
        return {'status': 'PASS'}
-
-
-def big_is_common_format(good_format):
-   """Check FP 2 - Common Format on large ontologies
-
-   Args:
-       good_format (bool): True if ontology could be parsed by Jena
-
-   Return:
-       PASS if good_format, ERROR otherwise.
-   """
-   if good_format is None:
-       return {'status': 'ERROR',
-               'comment': 'Unable to load ontology (may be too large)'}
-   elif good_format is False:
-       return {'status': 'ERROR',
-               'comment': 'Unable to parse ontology'}
    else:
-       return {'status': 'PASS'}
+       return {'status': 'WARN', 'comment': f'OWL syntax ({syntax}), but should be RDF/XML'}
 ```

principles/checks/fp_003.md

@@ -33,20 +33,19 @@ The full OBO Foundry ID Policy can be found [here](http://www.obofoundry.org/id-
 All entity IRIs are retrieved from the ontology, excluding annotation properties. Annotation properties may use hashtags and words due to legacy OBO conversions for subset properties. All other IRIs are checked if they are in the ontology's namespace. If the IRI begins with the ontology namespace, the next character must be an underscore. If not, this is an error. The IRI is also compared to a regex pattern to check if the local ID after the underscore is numeric. If not, this is a warning.
 
 ```python
-import dash_utils
 import os
 import re
 
-from dash_utils import format_msg
+import dash_utils
 
 iri_pattern = r'http:\/\/purl\.obolibrary\.org\/obo\/%s_[0-9]{1,9}'
 owl_deprecated = 'http://www.w3.org/2002/07/owl#deprecated'
 
-error_msg = '{0} invalid IRIs'
+error_msg = '{} invalid IRIs. The Ontology IRI is {}valid.'
 warn_msg = '{0} warnings on IRIs'
 
 
-def has_valid_uris(robot_gateway, namespace, ontology):
+def has_valid_uris(robot_gateway, namespace, ontology, ontology_dir):
    """Check FP 3 - URIs.
 
    This check ensures that all ontology entities follow NS_LOCALID.
@@ -67,6 +66,7 @@ def has_valid_uris(robot_gateway, namespace, ontology):
        otherwise.
    """
    if not ontology:
+       dash_utils.write_empty(os.path.join(ontology_dir, 'fp3.tsv'), ["Status", "Issue"])
        return {'status': 'ERROR', 'comment': 'Unable to load ontology'}
 
    entities = robot_gateway.OntologyHelper.getEntities(ontology)
@@ -95,10 +95,14 @@ def has_valid_uris(robot_gateway, namespace, ontology):
        elif check == 'WARN':
            warn.append(iri)
 
-   return save_invalid_uris(namespace, error, warn)
+   ontology_iri = dash_utils.get_ontology_iri(ontology)
+   
+   valid_iri = is_valid_ontology_iri(ontology_iri, namespace)
 
+   return save_invalid_uris(error, warn, ontology_dir, valid_iri)
 
-def big_has_valid_uris(namespace, file):
+
+def big_has_valid_uris(namespace, file, ontology_dir):
    """Check FP 3 - URIs on a big ontology.
 
    This check ensures that all ontology entities follow NS_LOCALID.
@@ -112,6 +116,7 @@ def big_has_valid_uris(namespace, file):
    Args:
        namespace (str): ontology ID
        file (str): path to ontology file
+       ontology_dir (str):
 
    Return:
        INFO if ontology IRIs cannot be parsed. ERROR if any errors, WARN if
@@ -134,6 +139,7 @@ def big_has_valid_uris(namespace, file):
            if 'Ontology' and 'about' in line:
                if not owl and not rdf:
                    # did not find OWL and RDF - end now
+                   dash_utils.write_empty(os.path.join(ontology_dir, 'fp3.tsv'), ["Status", "Issue"])
                    return {'status': 'ERROR',
                            'comment': 'Unable to parse ontology'}
 
@@ -171,11 +177,20 @@ def big_has_valid_uris(namespace, file):
 
    if not valid:
        # not valid ontology
+       dash_utils.write_empty(os.path.join(ontology_dir, 'fp3.tsv'), ["Status", "Issue"])
        return {'status': 'ERROR',
                'comment': 'Unable to parse ontology'}
 
-   return save_invalid_uris(namespace, error, warn)
+   return save_invalid_uris(error, warn, ontology_dir)
+
 
+def is_valid_ontology_iri(iri, namespace):
+   if iri:
+       if iri == 'http://purl.obolibrary.org/obo/{0}.owl'.format(namespace):
+           return True
+       if iri == 'http://purl.obolibrary.org/obo/{0}/{0}-base.owl'.format(namespace):
+           return True
+   return False
 
 def check_uri(namespace, iri):
    """Check if a given IRI is valid.
@@ -193,43 +208,52 @@ def check_uri(namespace, iri):
        return True
    if iri.startswith(namespace):
        # all NS IRIs must follow NS_
-       if not iri.startwith(namespace + '_'):
+       if not iri.startswith(namespace + '_'):
            return 'ERROR'
        # it is recommended to follow NS_NUMID
        elif not re.match(pattern, iri, re.IGNORECASE):
            return 'WARN'
    return True
 
 
-def save_invalid_uris(ns, error, warn):
+def save_invalid_uris(error, warn, ontology_dir, valid_ontology_iri = True):
    """Save invalid (error or warning) IRIs to a report file
-   (reports/dashboard/*/fp3.tsv).
 
    Args:
-       ns (str): ontology ID
        error (list): list of ERROR IRIs
        warn (list): list of WARN IRIs
+       ontology_dir (str):
 
    Return:
        ERROR or WARN with detailed message, or PASS if no errors or warnings.
    """
-   if len(error) > 0 or len(warn) > 0:
-       file = 'build/dashboard/{0}/fp3.tsv'.format(ns)
-       with open(file, 'w+') as f:
-           for e in error:
-               f.write('ERROR\t{0}\n'.format(e))
-           for w in warn:
-               f.write('WARN\t{0}\n'.format(w))
+   # write a report (maybe empty)
+   file = os.path.join(ontology_dir, 'fp3.tsv')
+
+   with open(file, 'w+') as f:
+       f.write('Status\tIssue\n')
+       for e in error:
+           f.write('ERROR\t{0}\n'.format(e))
+       for w in warn:
+           f.write('WARN\t{0}\n'.format(w))
+
+   o_iri_msg=""
+   if not valid_ontology_iri:
+       o_iri_msg = "not "
 
    if len(error) > 0 and len(warn) > 0:
        return {'status': 'ERROR',
                'file': 'fp3',
-               'comment': ' '.join([error_msg.format(len(error)),
+               'comment': ' '.join([error_msg.format(len(error), o_iri_msg),
                                     warn_msg.format(len(warn))])}
    elif len(error) > 0:
        return {'status': 'ERROR',
                'file': 'fp3',
-               'comment': error_msg.format(len(error))}
+               'comment': error_msg.format(len(error), o_iri_msg)}
+   elif not valid_ontology_iri:
+       return {'status': 'ERROR',
+               'file': 'fp3',
+               'comment': error_msg.format(0, o_iri_msg)}
    elif len(warn) > 0:
        return {'status': 'ERROR',
                'file': 'fp3',