Add datatype QC for annotations related to date (#2066)

* add datetime datatype QC * replace string to datetime in date related properties * update illegal date violation from ODK 1.5 * replace string to datetime on date related annotations --------- Co-authored-by: Anita Caron <[email protected]>
obophenotype · May 21, 2024 · 7990aa5 · 7990aa5
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diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml
@@ -29,5 +29,5 @@ jobs:
       - name: Run ontology QC checks
         env:
           DEFAULT_BRANCH: master
-        run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false
+        run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false MIR=false
 
diff --git a/docs/odk-workflows/ManageDocumentation.md b/docs/odk-workflows/ManageDocumentation.md
@@ -43,5 +43,3 @@ The documentation is _not_ automatically updated from the Markdown, and needs to
 3. Just to double check, you can now navigate to your documentation pages (usually https://obophenotype.github.io/cell-ontology/). 
    Just make sure you give GitHub 2-5 minutes to build the pages!
 
-
-
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -10,7 +10,7 @@
 # More information: https://github.com/INCATools/ontology-development-kit/
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                3ef44073feb4dd21f093356b564a51bd94638e4a757ed43c0c9ff69e9599cac2
+CONFIG_HASH=                8b5b779b91f8bb931caf3512d6c7fcb325ef83bafc7ba409b86058a9dae7f67f
 
 
 # ----------------------------------------
@@ -44,7 +44,7 @@ REPORT_FAIL_ON =            ERROR
 REPORT_LABEL =              
 REPORT_PROFILE_OPTS =       
 OBO_FORMAT_OPTIONS =        
-SPARQL_VALIDATION_CHECKS =  equivalent-classes owldef-self-reference nolabels pmid-not-dbxref obsolete-replaced_by obsolete-alt-id orcid-contributor illegal-annotation-property label-synonym-polysemy 
+SPARQL_VALIDATION_CHECKS =  equivalent-classes owldef-self-reference nolabels pmid-not-dbxref obsolete-replaced_by obsolete-alt-id orcid-contributor illegal-annotation-property label-synonym-polysemy illegal-date 
 SPARQL_EXPORTS =            basic-report 
 ODK_VERSION_MAKEFILE =      v1.5
 

diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl
diff --git a/src/ontology/cl-odk.yaml b/src/ontology/cl-odk.yaml
@@ -111,6 +111,7 @@ robot_report:
     - orcid-contributor
     - illegal-annotation-property
     - label-synonym-polysemy
+    - illegal-date
   custom_sparql_exports :
     - basic-report
 components:

diff --git a/src/sparql/illegal-date-violation.sparql b/src/sparql/illegal-date-violation.sparql
@@ -0,0 +1,12 @@
+PREFIX dct: <http://purl.org/dc/terms/>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
+
+SELECT DISTINCT ?term ?property ?value WHERE
+{
+  VALUES ?property {dct:date dct:issued dct:created oboInOwl:creation_date}
+  ?term ?property ?value .
+  FILTER (datatype(?value) != xsd:date || !regex(str(?value), '^\\d{4}-\\d\\d-\\d\\d$'))
+  FILTER (datatype(?value) != xsd:dateTime || !regex(str(?value), '^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}Z'))
+}
+
diff --git a/src/sparql/replace_string_to_datetime.ru b/src/sparql/replace_string_to_datetime.ru
@@ -0,0 +1,21 @@
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX dct: <http://purl.org/dc/terms/>
+PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
+
+DELETE {
+	?sub ?property ?value .
+}
+
+INSERT {
+    ?sub ?property ?new_value.
+}
+
+WHERE {
+    VALUES ?property {dct:date dct:issued dct:created oboInOwl:creation_date}
+    ?sub ?property ?value .
+    FILTER(Datatype(?value)!=xsd:dateTime)
+    BIND(STRDT(?value, xsd:dateTime) as ?new_value)
+}
Original file line number	Diff line number	Diff line change
Expand Up		@@ -43,5 +43,3 @@ The documentation is _not_ automatically updated from the Markdown, and needs to
		3. Just to double check, you can now navigate to your documentation pages (usually https://obophenotype.github.io/cell-ontology/).
		Just make sure you give GitHub 2-5 minutes to build the pages!