ISA profile: fixed some issues and removed leftover code

Author: floWetzels

rocrate_validator/profiles/isa-ro-crate/2_assay.ttl

@@ -93,7 +93,7 @@ isa-ro-crate:AssayMustHaveBaseDescriptors a sh:NodeShape ;
 
 
 isa-ro-crate:AssayMustBeReferencedFromInvestigation a sh:NodeShape ;
-  sh:name "Assay MUST be directly referenced from Investigation or Study (Root Data Entity)" ;
+  sh:name "Assay MUST be directly referenced from Investigation (Root Data Entity) or Study" ;
   sh:targetClass isa-ro-crate:Assay ;
   sh:property[
         a sh:PropertyShape ;
@@ -105,7 +105,7 @@ isa-ro-crate:AssayMustBeReferencedFromInvestigation a sh:NodeShape ;
             ) ;
         ] ;
         sh:qualifiedMinCount 1 ;
-        sh:name "Assay MUST be directly referenced from Investigation or Study (Root Data Entity)" ;
+        sh:name "Assay MUST be directly referenced from Investigation (Root Data Entity) or Study" ;
         sh:description """Check if the Assay is directly linked to the Investigation (which is the Root Data Entity) or a Study using the `hasPart` (as defined in `schema.org`) property" """ ;
         sh:message "Assay MUST be directly referenced in hasPart on the Investigation (Root Data Entity) or a Study"
     ]

rocrate_validator/profiles/isa-ro-crate/4_protocol.ttl

@@ -98,8 +98,8 @@ isa-ro-crate:ProtocolShouldHaveIntendedUse a sh:NodeShape ;
             [sh:datatype xsd:string]
             [sh:class schema:DefinedTerm]
         ) ;
-        sh:description "Check that if protocol does have at least one intended use, it MUST be of type DefinedTerm" ;
-        sh:message "Protocol intended use MUST be of type DefinedTerm" ;
+        sh:description "Check that if protocol does have at least one intended use, it MUST be of type string or DefinedTerm" ;
+        sh:message "Protocol intended use MUST be of type string or DefinedTerm" ;
         sh:severity sh:Violation ;
     ]
 .

rocrate_validator/profiles/isa-ro-crate/5_sample.ttl

@@ -54,9 +54,6 @@ isa-ro-crate:SampleShouldHaveAdditionalPropertyOfCorrectType a sh:NodeShape ;
         a sh:PropertyShape ;
         sh:path bioschemas-prop:additionalProperty ;
         sh:minCount 1 ;
-        sh:not [
-            sh:hasValue ""
-        ] ;
         sh:description "Check that sample does have at least one additional property" ;
         sh:message "Sample entity SHOULD have at least one additional property" ;
         sh:severity sh:Warning ;

rocrate_validator/profiles/isa-ro-crate/7_person.ttl

@@ -54,9 +54,6 @@ isa-ro-crate:PersonShouldHaveAffiliationOfCorrectType a sh:NodeShape ;
         a sh:PropertyShape ;
         sh:path schema:affiliation ;
         sh:minCount 1 ;
-        sh:not [
-            sh:hasValue ""
-        ] ;
         sh:description "Check that person does have at least one affiliation" ;
         sh:message "Person entity SHOULD have at least one affiliation" ;
         sh:severity sh:Warning ;
@@ -79,9 +76,6 @@ isa-ro-crate:PersonShouldHaveJobTitleOfCorrectType a sh:NodeShape ;
         a sh:PropertyShape ;
         sh:path schema:jobTitle ;
         sh:minCount 1 ;
-        sh:not [
-            sh:hasValue ""
-        ] ;
         sh:description "Check that person does have at least one job title" ;
         sh:message "Person entity SHOULD have at least one job title" ;
         sh:severity sh:Warning ;

rocrate_validator/profiles/isa-ro-crate/8_article.ttl

@@ -73,9 +73,6 @@ isa-ro-crate:ArticleShouldHaveAuthorOfCorrectType a sh:NodeShape ;
         a sh:PropertyShape ;
         sh:path schema:author ;
         sh:minCount 1 ;
-        sh:not [
-            sh:hasValue ""
-        ] ;
         sh:description "Check that article does have at least one author" ;
         sh:message "Article entity SHOULD have at least one author" ;
         sh:severity sh:Warning ;