Scripts for local file migrations. Closes #642.

migration/v11.0/README.md

@@ -0,0 +1,62 @@
+# Migrating to gist v11.0
+
+See also, additional documentation in the file `docs/MajorVersionMigration.md`.
+
+This file gives a quick overview of using the migration utilities provided
+by the gist team to help migrate from version v10 of gist. These
+utilities should be reviewed before running them to make sure you approve
+of the actions prior to using them.
+
+These utilities do not handle everything, in some cases we can only warn you
+about changes that were made in gist and you will need to decide how you want
+to handle the changes.
+
+## Migration Queries
+
+All of our migration tools are SPARQL queries.
+
+You will note that some files have very similar names. Here is what the suffixes mean:
+- `_default.rq` : These queries only work on the default graph`*`
+- `_ngraphs.rq` : These queries only work on named graphs
+- `.rq` : These queries work on both the default graph and named graphs
+
+`*` the handling of these queries will be dependent upon which Triplestore
+you are using and how it was configured. Some Triplestores will only use
+triples in the default graph, some will use all triples in all named graphs.
+
+## Requirements
+
+These migration scripts are meant to be run using the open source onto_tool
+program. Information about onto_tool and how to install it, is available at
+[github](https://github.com/semanticarts/ontology-toolkit).
+
+## Run on local files
+
+NOTE: A known limitation of `onto_tool` is that it does not support named graphs when run against local files.
+It does support named graphs when run against a SPARQL endpoint.
+
+Start in this directory.
+
+Put source data files in the ./input/ directory. See the onto_tool documentation for which file formats are supported.
+
+Execute:
+```shell
+onto_tool bundle migrate_local.yaml
+```
+
+Output files will be created in the ./output/ directory.
+
+Report files will be created in the ./reports/ directory.
+
+## Run on a SPARQL Endpoint
+
+You will need to tell onto_tool the URL of your SPARQL endpoint. You can do that
+by editing the migration_endpoint.yaml file, or you can put it into the command
+line execution like this:
+
+```shell
+onto_tool bundle -v user USER -v password PWD
+                 -v endpoint ENDPOINT-URI
+                 [ -v update_endpoint UPDATE-URI ]
+                 -v report REPORT-DIR migrate_endpoint.yaml
+```

migration/v11.0/action_rename_default.rq

@@ -0,0 +1,27 @@
+prefix gist: <https://ontologies.semanticarts.com/gist/>
+
+DELETE {
+    ?oldTerm ?sp ?so .
+    ?ps ?oldTerm ?po .
+    ?os ?op ?oldTerm .
+}
+INSERT {
+    ?newTerm ?sp ?so .
+    ?ps ?newTerm ?po .
+    ?os ?op ?newTerm .
+}
+where {
+    values (?oldTerm ?newTerm) {
+        (gist:ContemporaneousEvent gist:ContemporaryEvent)
+        (gist:hasOrderedMember gist:hasMember)
+        (gist:baseConversionFactor gist:conversionFactor)
+        (gist:standardConversionFactor gist:conversionFactor)
+    }
+    {
+        ?oldTerm ?sp ?so
+    } UNION {
+        ?ps ?oldTerm ?po
+    } UNION {
+        ?os ?op ?oldTerm
+    }
+}

migration/v11.0/action_rename_ngraphs.rq

@@ -0,0 +1,33 @@
+prefix gist: <https://ontologies.semanticarts.com/gist/>
+
+DELETE {
+    graph ?graph {
+        ?oldTerm ?sp ?so .
+        ?ps ?oldTerm ?po .
+        ?os ?op ?oldTerm .
+    }
+}
+INSERT {
+    graph ?graph {
+        ?newTerm ?sp ?so .
+        ?ps ?newTerm ?po .
+        ?os ?op ?newTerm .
+    }
+}
+where {
+    values (?oldTerm ?newTerm) {
+        (gist:ContemporaneousEvent gist:ContemporaryEvent)
+        (gist:hasOrderedMember gist:hasMember)
+        (gist:baseConversionFactor gist:conversionFactor)
+        (gist:standardConversionFactor gist:conversionFactor)
+    }
+    graph ?graph {
+        {
+            ?oldTerm ?sp ?so
+        } UNION {
+            ?ps ?oldTerm ?po
+        } UNION {
+            ?os ?op ?oldTerm
+        }
+    }
+}

migration/v11.0/detect_domain_changed.rq

@@ -0,0 +1,44 @@
+prefix skos: <http://www.w3.org/2004/02/skos/core#>
+prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+prefix sh: <http://www.w3.org/ns/shacl#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+prefix gist: <https://ontologies.semanticarts.com/gist/>
+
+CONSTRUCT {
+    ?report a sh:ValidationReport ;
+        sh:conforms false ;
+        sh:result
+            [
+                a sh:ValidationResult ;
+                sh:focusNode ?modified ;
+                sh:resultMessage ?error ;
+                sh:resultSeverity sh:Warning ;
+                sh:sourceConstraintComponent <urn:constraint:range-removed-entity>
+            ] .
+}
+WHERE {
+    {
+        select distinct ?modified where {
+            values ?modified {
+                gist:usesTimeZoneStandard
+            }
+            {
+                ?s ?modified ?o
+            } UNION {
+                ?s ?p ?modified
+            } UNION {
+                ?modified ?p ?o
+            } UNION {
+                graph ?g { ?s ?modified ?o }
+            } UNION {
+                graph ?g { ?s ?p ?modified }
+            } UNION {
+                graph ?g { ?modified ?p ?o }
+            }
+        }
+    }
+    bind(<urn:range-removed-entity-validation-report> as ?report)
+    bind(CONCAT("WARNING: a rdfs:domain of property gist:",
+        REPLACE(STR(?modified), '^.*[/#]', ''), " was removed. If you were relying on ",
+        "inference from the removed domain you will need to address this change." ) as ?error)
+}

migration/v11.0/detect_domain_changed_default.rq

@@ -0,0 +1,44 @@
+prefix skos: <http://www.w3.org/2004/02/skos/core#>
+prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+prefix sh: <http://www.w3.org/ns/shacl#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+prefix gist: <https://ontologies.semanticarts.com/gist/>
+
+CONSTRUCT {
+    ?report a sh:ValidationReport ;
+        sh:conforms false ;
+        sh:result
+            [
+                a sh:ValidationResult ;
+                sh:focusNode ?modified ;
+                sh:resultMessage ?error ;
+                sh:resultSeverity sh:Warning ;
+                sh:sourceConstraintComponent <urn:constraint:range-removed-entity>
+            ] .
+}
+WHERE {
+    {
+        select distinct ?modified where {
+            values ?modified {
+                gist:usesTimeZoneStandard
+            }
+            {
+                ?s ?modified ?o
+            } UNION {
+                ?s ?p ?modified
+            } UNION {
+                ?modified ?p ?o
+#            } UNION {
+#                graph ?g { ?s ?modified ?o }
+#            } UNION {
+#                graph ?g { ?s ?p ?modified }
+#            } UNION {
+#                graph ?g { ?modified ?p ?o }
+            }
+        }
+    }
+    bind(<urn:range-removed-entity-validation-report> as ?report)
+    bind(CONCAT("WARNING: a rdfs:domain of property gist:",
+        REPLACE(STR(?modified), '^.*[/#]', ''), " was removed. If you were relying on ",
+        "inference from the removed domain you will need to address this change." ) as ?error)
+}

migration/v11.0/detect_removed.rq

@@ -0,0 +1,75 @@
+prefix skos: <http://www.w3.org/2004/02/skos/core#>
+prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+prefix sh: <http://www.w3.org/ns/shacl#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+prefix gist: <https://ontologies.semanticarts.com/gist/>
+
+CONSTRUCT {
+    ?report a sh:ValidationReport ;
+        sh:conforms false ;
+        sh:result
+            [
+                a sh:ValidationResult ;
+                sh:focusNode ?deleted ;
+                sh:resultMessage ?error ;
+                sh:resultSeverity sh:Warning ;
+                sh:sourceConstraintComponent <urn:constraint:removed-entity>
+            ] .
+}
+WHERE {
+    {
+        select distinct ?deleted where {
+            values ?deleted {
+                ## Time Model Classes
+                gist:TimeInstant
+                gist:DateInstant
+                gist:GreenwichInstant
+                gist:HumanInstant
+                gist:LocalInstant
+                gist:SystemInstant
+
+                ## Time Model Properties
+                gist:hasEnd
+                gist:hasActual
+                gist:hasActualEnd
+                gist:hasPlannedEnd
+                gist:hasDeathDate
+                gist:hasStart
+                gist:hasActualStart
+                gist:hasPlanned
+                gist:hasBirthDate
+                gist:hasPlannedStart
+                gist:epoch
+                gist:localDate
+                gist:localDateTime
+                gist:localTime
+                gist:universalDate
+                gist:universalDateTime
+                gist:universalTime
+                gist:isSameTimeAs
+                gist:wasLastModifiedAt
+
+                ## Misc
+                # gist:hasOrderedMember
+                gist:hasBiologicalOffspring
+            }
+            {
+                ?s ?deleted ?o
+            } UNION {
+                ?s ?p ?deleted
+            } UNION {
+                ?deleted ?p ?o
+            } UNION {
+                graph ?g { ?s ?deleted ?o }
+            } UNION {
+                graph ?g { ?s ?p ?deleted }
+            } UNION {
+                graph ?g { ?deleted ?p ?o }
+            }
+        }
+    }
+    bind(<urn:deleted-entity-validation-report> as ?report)
+    bind(CONCAT("Removed entity gist:",
+        REPLACE(STR(?deleted), '^.*[/#]', ''), " referenced in data. ",
+        "Review release notes for information about the changes.") as ?error)
+}

migration/v11.0/detect_removed_default.rq

@@ -0,0 +1,75 @@
+prefix skos: <http://www.w3.org/2004/02/skos/core#>
+prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+prefix sh: <http://www.w3.org/ns/shacl#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+prefix gist: <https://ontologies.semanticarts.com/gist/>
+
+CONSTRUCT {
+    ?report a sh:ValidationReport ;
+        sh:conforms false ;
+        sh:result
+            [
+                a sh:ValidationResult ;
+                sh:focusNode ?deleted ;
+                sh:resultMessage ?error ;
+                sh:resultSeverity sh:Warning ;
+                sh:sourceConstraintComponent <urn:constraint:removed-entity>
+            ] .
+}
+WHERE {
+    {
+        select distinct ?deleted where {
+            values ?deleted {
+                ## Time Model Classes
+                gist:TimeInstant
+                gist:DateInstant
+                gist:GreenwichInstant
+                gist:HumanInstant
+                gist:LocalInstant
+                gist:SystemInstant
+
+                ## Time Model Properties
+                gist:hasEnd
+                gist:hasActual
+                gist:hasActualEnd
+                gist:hasPlannedEnd
+                gist:hasDeathDate
+                gist:hasStart
+                gist:hasActualStart
+                gist:hasPlanned
+                gist:hasBirthDate
+                gist:hasPlannedStart
+                gist:epoch
+                gist:localDate
+                gist:localDateTime
+                gist:localTime
+                gist:universalDate
+                gist:universalDateTime
+                gist:universalTime
+                gist:isSameTimeAs
+                gist:wasLastModifiedAt
+
+                ## Misc
+                # gist:hasOrderedMember
+                gist:hasBiologicalOffspring
+            }
+            {
+                ?s ?deleted ?o
+            } UNION {
+                ?s ?p ?deleted
+            } UNION {
+                ?deleted ?p ?o
+#            } UNION {
+#                graph ?g { ?s ?deleted ?o }
+#            } UNION {
+#                graph ?g { ?s ?p ?deleted }
+#            } UNION {
+#                graph ?g { ?deleted ?p ?o }
+            }
+        }
+    }
+    bind(<urn:deleted-entity-validation-report> as ?report)
+    bind(CONCAT("Removed entity gist:",
+        REPLACE(STR(?deleted), '^.*[/#]', ''), " referenced in data. ",
+        "Review release notes for information about the changes.") as ?error)
+}