Merge branch 'master' into ontology-review/system

ge-high-assurance · Feb 3, 2021 · 6ee3dd1 · 6ee3dd1
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diff --git a/.chglog/CHANGELOG.md b/.chglog/CHANGELOG.md
@@ -0,0 +1,232 @@
+<a name="unreleased"></a>
+## [Unreleased]
+
+
+<a name="v5.0"></a>
+## [v5.0] - 2021-02-02
+### Cli
+- use dev requirements from the dev/ directory
+- add wheel for nix users
+- fix some pylint warnings
+- set epoch in shell.nix to avoid zip errors
+- add requirements-dev for dev dependencies
+
+### Reverts
+- cli: add requirements-dev for dev dependencies
+
+### Pull Requests
+- Merge pull request [#279](https://github.com/ge-high-assurance/RACK/issues/279) from ge-high-assurance/ks/queryNodegroups
+- Merge pull request [#253](https://github.com/ge-high-assurance/RACK/issues/253) from ge-high-assurance/turnstile_assist
+- Merge pull request [#250](https://github.com/ge-high-assurance/RACK/issues/250) from ge-high-assurance/ontology-review/agents
+- Merge pull request [#263](https://github.com/ge-high-assurance/RACK/issues/263) from ge-high-assurance/ontology-review/testing
+- Merge pull request [#249](https://github.com/ge-high-assurance/RACK/issues/249) from ge-high-assurance/assist_file_updates
+- Merge pull request [#251](https://github.com/ge-high-assurance/RACK/issues/251) from ge-high-assurance/ji/composite-action
+
+
+<a name="v4.1"></a>
+## [v4.1] - 2020-12-17
+### Pull Requests
+- Merge pull request [#248](https://github.com/ge-high-assurance/RACK/issues/248) from ge-high-assurance/em/wasDerivedFrom
+- Merge pull request [#247](https://github.com/ge-high-assurance/RACK/issues/247) from ge-high-assurance/em/str-uri
+- Merge pull request [#237](https://github.com/ge-high-assurance/RACK/issues/237) from ge-high-assurance/em/str-overlay
+
+
+<a name="v4.0"></a>
+## [v4.0] - 2020-12-07
+### Assist
+- update documentation
+- update documentation
+
+### Pull Requests
+- Merge pull request [#242](https://github.com/ge-high-assurance/RACK/issues/242) from ge-high-assurance/glguy-patch-1
+
+
+<a name="v3.9"></a>
+## [v3.9] - 2020-12-03
+### Assist
+- remove generated Prolog files, update doc
+
+### Ci
+- Test RACK with pytest
+- Don't allow failure in ontology linting step
+- Package RACK CLI and requirements as wheels
+- Always build RACK-box image, only publish from master branch
+
+### Databin
+- fix bash loop over empty strings
+- gcc wrapper support other extensions
+
+### Pull Requests
+- Merge pull request [#241](https://github.com/ge-high-assurance/RACK/issues/241) from ge-high-assurance/em/restore-components
+- Merge pull request [#239](https://github.com/ge-high-assurance/RACK/issues/239) from ge-high-assurance/ji/combine-workflows
+- Merge pull request [#236](https://github.com/ge-high-assurance/RACK/issues/236) from ge-high-assurance/em/when-then
+- Merge pull request [#235](https://github.com/ge-high-assurance/RACK/issues/235) from ge-high-assurance/am-assuranceUpdate
+- Merge pull request [#234](https://github.com/ge-high-assurance/RACK/issues/234) from ge-high-assurance/em/provenance-example
+- Merge pull request [#232](https://github.com/ge-high-assurance/RACK/issues/232) from ge-high-assurance/vr/gcc-wrapper
+- Merge pull request [#233](https://github.com/ge-high-assurance/RACK/issues/233) from ge-high-assurance/em/integrate-grammatech
+- Merge pull request [#227](https://github.com/ge-high-assurance/RACK/issues/227) from ge-high-assurance/TurnstileUpdates
+- Merge pull request [#230](https://github.com/ge-high-assurance/RACK/issues/230) from ge-high-assurance/AM-HotFix
+- Merge pull request [#228](https://github.com/ge-high-assurance/RACK/issues/228) from ge-high-assurance/em/gramma-tech-failure-reason
+- Merge pull request [#225](https://github.com/ge-high-assurance/RACK/issues/225) from ge-high-assurance/am-assurance
+- Merge pull request [#222](https://github.com/ge-high-assurance/RACK/issues/222) from ge-high-assurance/AmbigousPropertiesHotFix
+- Merge pull request [#217](https://github.com/ge-high-assurance/RACK/issues/217) from ge-high-assurance/Issue[#157](https://github.com/ge-high-assurance/RACK/issues/157)-TurnstileUpdates
+- Merge pull request [#218](https://github.com/ge-high-assurance/RACK/issues/218) from ge-high-assurance/ji/tweak-ci
+- Merge pull request [#207](https://github.com/ge-high-assurance/RACK/issues/207) from ge-high-assurance/em/identified-enums
+- Merge pull request [#211](https://github.com/ge-high-assurance/RACK/issues/211) from ge-high-assurance/MasterCleanUp
+- Merge pull request [#210](https://github.com/ge-high-assurance/RACK/issues/210) from ge-high-assurance/em/directory-cleanup
+- Merge pull request [#208](https://github.com/ge-high-assurance/RACK/issues/208) from ge-high-assurance/em/grammatech
+- Merge pull request [#203](https://github.com/ge-high-assurance/RACK/issues/203) from ge-high-assurance/am/queryStr
+- Merge pull request [#199](https://github.com/ge-high-assurance/RACK/issues/199) from ge-high-assurance/lb/always-build-rack-box
+
+
+<a name="v3.0"></a>
+## [v3.0] - 2020-10-23
+### Ci
+- Lint every branch, not just master
+- Remove duplicated Packer build configuration
+- Use the Prolog "check" tool to lint the ontology
+
+### Pull Requests
+- Merge pull request [#184](https://github.com/ge-high-assurance/RACK/issues/184) from ge-high-assurance/add_assist_to_dist
+- Merge pull request [#186](https://github.com/ge-high-assurance/RACK/issues/186) from ge-high-assurance/fix_copyright_notices
+
+
+<a name="v2.9"></a>
+## [v2.9] - 2020-10-20
+### Ci
+- Minimize the source tarball for the Packer image
+- Use `type -P`, not `command -v`
+- Require manual download of Packer for use with `act`
+- Document running Github Actions workflows locally with `act`
+
+### Packer
+- Update documentation to reflect the new build process
+- reuse setup-rack.sh
+
+### Prolog
+- add graphviz-based visualization script
+- add missing utils/float_equality
+- add BDU checks
+- fix pldoc problem
+- use a prolog:message in write_ontology
+- add generated ontology/confidence.pl
+- document transitive_closure/3
+- add utils to documentation
+- carve out and generalize zip_by_key
+- print out written files in write_ontology
+- auto-generate ontology classes/predicates
+- fix pldoc comment
+- reorganize codebase, more abstract paths
+- improve help message
+- use module rack_model in common_opts
+- add paths.pl and a hazard query
+
+### Pull Requests
+- Merge pull request [#180](https://github.com/ge-high-assurance/RACK/issues/180) from ge-high-assurance/ji/add-rack-box
+- Merge pull request [#175](https://github.com/ge-high-assurance/RACK/issues/175) from ge-high-assurance/em/copyright
+- Merge pull request [#178](https://github.com/ge-high-assurance/RACK/issues/178) from ge-high-assurance/updateCSV
+- Merge pull request [#174](https://github.com/ge-high-assurance/RACK/issues/174) from ge-high-assurance/am/uniqueIdentifier
+- Merge pull request [#173](https://github.com/ge-high-assurance/RACK/issues/173) from ge-high-assurance/sadl2owl
+- Merge pull request [#130](https://github.com/ge-high-assurance/RACK/issues/130) from ge-high-assurance/file_creation_activity
+- Merge pull request [#154](https://github.com/ge-high-assurance/RACK/issues/154) from ge-high-assurance/dataproc
+- Merge pull request [#156](https://github.com/ge-high-assurance/RACK/issues/156) from ge-high-assurance/em/clear-nodegroups-on-setup
+- Merge pull request [#155](https://github.com/ge-high-assurance/RACK/issues/155) from ge-high-assurance/load-order
+- Merge pull request [#151](https://github.com/ge-high-assurance/RACK/issues/151) from ge-high-assurance/em/bdu-notes
+
+
+<a name="v2.0"></a>
+## [v2.0] - 2020-08-27
+
+<a name="v1.9"></a>
+## [v1.9] - 2020-08-25
+### Cli
+- don't require a command
+- Update semtk-python3 in requirements.txt
+
+### Ontology
+- add confidence meta-model
+
+### Pull Requests
+- Merge pull request [#120](https://github.com/ge-high-assurance/RACK/issues/120) from ge-high-assurance/vr/confidence
+- Merge pull request [#139](https://github.com/ge-high-assurance/RACK/issues/139) from ge-high-assurance/Issue[#109](https://github.com/ge-high-assurance/RACK/issues/109)
+- Merge pull request [#134](https://github.com/ge-high-assurance/RACK/issues/134) from ge-high-assurance/assessment
+- Merge pull request [#133](https://github.com/ge-high-assurance/RACK/issues/133) from ge-high-assurance/lb/software-queries
+- Merge pull request [#137](https://github.com/ge-high-assurance/RACK/issues/137) from ge-high-assurance/hazard_identified
+- Merge pull request [#136](https://github.com/ge-high-assurance/RACK/issues/136) from ge-high-assurance/class_def
+- Merge pull request [#135](https://github.com/ge-high-assurance/RACK/issues/135) from ge-high-assurance/turnstile_make_targets
+- Merge pull request [#126](https://github.com/ge-high-assurance/RACK/issues/126) from ge-high-assurance/em/ingest-component
+- Merge pull request [#123](https://github.com/ge-high-assurance/RACK/issues/123) from ge-high-assurance/em/cli-script
+- Merge pull request [#122](https://github.com/ge-high-assurance/RACK/issues/122) from ge-high-assurance/em/compile-subtyping
+- Merge pull request [#118](https://github.com/ge-high-assurance/RACK/issues/118) from ge-high-assurance/am/reqstr
+- Merge pull request [#93](https://github.com/ge-high-assurance/RACK/issues/93) from ge-high-assurance/vr/delete-nodegroups
+- Merge pull request [#92](https://github.com/ge-high-assurance/RACK/issues/92) from ge-high-assurance/vr/list-nodegroups
+- Merge pull request [#110](https://github.com/ge-high-assurance/RACK/issues/110) from ge-high-assurance/em/flat-file
+- Merge pull request [#83](https://github.com/ge-high-assurance/RACK/issues/83) from ge-high-assurance/em/qualified-usage
+- Merge pull request [#99](https://github.com/ge-high-assurance/RACK/issues/99) from ge-high-assurance/em/metadata
+
+
+<a name="v1.0"></a>
+## [v1.0] - 2020-08-01
+
+<a name="v0.9"></a>
+## [v0.9] - 2020-07-29
+### TurnstileSystem
+- Fix typo (LANGAUGE -> LANGUAGE)
+- Revert changes to INTERFACE.csv
+- Update CSV files
+- Executable uses createBy, not wasGeneratedBy
+- Add CSV files
+- Add software structure classes to GenerateCSV
+- Add CounterApplicationUnitTesting
+- Add software sources
+
+### TurnstyleSystem
+- Add uniqueIdentifier to every class
+- Add structure of counter application to SADL
+
+### Pull Requests
+- Merge pull request [#91](https://github.com/ge-high-assurance/RACK/issues/91) from ge-high-assurance/vr/fix-type-of-with-status
+- Merge pull request [#88](https://github.com/ge-high-assurance/RACK/issues/88) from ge-high-assurance/vr/with-status-decorator
+- Merge pull request [#87](https://github.com/ge-high-assurance/RACK/issues/87) from ge-high-assurance/vr/nicer-output
+- Merge pull request [#86](https://github.com/ge-high-assurance/RACK/issues/86) from ge-high-assurance/vr/colorful-output
+- Merge pull request [#85](https://github.com/ge-high-assurance/RACK/issues/85) from ge-high-assurance/vr/trim-slash-in-base-url
+- Merge pull request [#82](https://github.com/ge-high-assurance/RACK/issues/82) from ge-high-assurance/branchForIssue47
+- Merge pull request [#80](https://github.com/ge-high-assurance/RACK/issues/80) from ge-high-assurance/lb/control-flow
+- Merge pull request [#77](https://github.com/ge-high-assurance/RACK/issues/77) from ge-high-assurance/lb/script-improvements
+- Merge pull request [#65](https://github.com/ge-high-assurance/RACK/issues/65) from ge-high-assurance/em/temporal
+- Merge pull request [#51](https://github.com/ge-high-assurance/RACK/issues/51) from ge-high-assurance/em/agents
+- Merge pull request [#60](https://github.com/ge-high-assurance/RACK/issues/60) from ge-high-assurance/lb/functions
+- Merge pull request [#41](https://github.com/ge-high-assurance/RACK/issues/41) from ge-high-assurance/em/software-ingestion-templates
+- Merge pull request [#30](https://github.com/ge-high-assurance/RACK/issues/30) from langston-barrett/lb/turnstile
+- Merge pull request [#36](https://github.com/ge-high-assurance/RACK/issues/36) from ge-high-assurance/em/software-ingestion
+- Merge pull request [#50](https://github.com/ge-high-assurance/RACK/issues/50) from ge-high-assurance/em/remove-properties-sadl
+
+
+<a name="v0.1"></a>
+## [v0.1] - 2020-07-02
+
+<a name="v0.0"></a>
+## v0.0 - 2020-06-29
+### TurnstileSystem
+- Remove Sample2.sadl
+- Fix typo (TurnStiles -> Turnstiles)
+
+### Pull Requests
+- Merge pull request [#33](https://github.com/ge-high-assurance/RACK/issues/33) from ge-high-assurance/em/project-file
+- Merge pull request [#26](https://github.com/ge-high-assurance/RACK/issues/26) from ge-high-assurance/em/uniqueIdentifier
+- Merge pull request [#15](https://github.com/ge-high-assurance/RACK/issues/15) from ge-high-assurance/AssuranceOntologyModel
+- Merge pull request [#2](https://github.com/ge-high-assurance/RACK/issues/2) from ge-high-assurance/lb/merge
+
+
+[Unreleased]: https://github.com/ge-high-assurance/RACK/compare/v5.0...HEAD
+[v5.0]: https://github.com/ge-high-assurance/RACK/compare/v4.1...v5.0
+[v4.1]: https://github.com/ge-high-assurance/RACK/compare/v4.0...v4.1
+[v4.0]: https://github.com/ge-high-assurance/RACK/compare/v3.9...v4.0
+[v3.9]: https://github.com/ge-high-assurance/RACK/compare/v3.0...v3.9
+[v3.0]: https://github.com/ge-high-assurance/RACK/compare/v2.9...v3.0
+[v2.9]: https://github.com/ge-high-assurance/RACK/compare/v2.0...v2.9
+[v2.0]: https://github.com/ge-high-assurance/RACK/compare/v1.9...v2.0
+[v1.9]: https://github.com/ge-high-assurance/RACK/compare/v1.0...v1.9
+[v1.0]: https://github.com/ge-high-assurance/RACK/compare/v0.9...v1.0
+[v0.9]: https://github.com/ge-high-assurance/RACK/compare/v0.1...v0.9
+[v0.1]: https://github.com/ge-high-assurance/RACK/compare/v0.0...v0.1
diff --git a/.chglog/CHANGELOG.tpl.md b/.chglog/CHANGELOG.tpl.md
@@ -0,0 +1,56 @@
+{{ if .Versions -}}
+<a name="unreleased"></a>
+## [Unreleased]
+
+{{ if .Unreleased.CommitGroups -}}
+{{ range .Unreleased.CommitGroups -}}
+### {{ .Title }}
+{{ range .Commits -}}
+- {{ if .Scope }}**{{ .Scope }}:** {{ end }}{{ .Subject }}
+{{ end }}
+{{ end -}}
+{{ end -}}
+{{ end -}}
+
+{{ range .Versions }}
+<a name="{{ .Tag.Name }}"></a>
+## {{ if .Tag.Previous }}[{{ .Tag.Name }}]{{ else }}{{ .Tag.Name }}{{ end }} - {{ datetime "2006-01-02" .Tag.Date }}
+{{ range .CommitGroups -}}
+### {{ .Title }}
+{{ range .Commits -}}
+- {{ if .Scope }}**{{ .Scope }}:** {{ end }}{{ .Subject }}
+{{ end }}
+{{ end -}}
+
+{{- if .RevertCommits -}}
+### Reverts
+{{ range .RevertCommits -}}
+- {{ .Revert.Header }}
+{{ end }}
+{{ end -}}
+
+{{- if .MergeCommits -}}
+### Pull Requests
+{{ range .MergeCommits -}}
+- {{ .Header }}
+{{ end }}
+{{ end -}}
+
+{{- if .NoteGroups -}}
+{{ range .NoteGroups -}}
+### {{ .Title }}
+{{ range .Notes }}
+{{ .Body }}
+{{ end }}
+{{ end -}}
+{{ end -}}
+{{ end -}}
+
+{{- if .Versions }}
+[Unreleased]: {{ .Info.RepositoryURL }}/compare/{{ $latest := index .Versions 0 }}{{ $latest.Tag.Name }}...HEAD
+{{ range .Versions -}}
+{{ if .Tag.Previous -}}
+[{{ .Tag.Name }}]: {{ $.Info.RepositoryURL }}/compare/{{ .Tag.Previous.Name }}...{{ .Tag.Name }}
+{{ end -}}
+{{ end -}}
+{{ end -}}
diff --git a/.chglog/config.yml b/.chglog/config.yml
@@ -0,0 +1,28 @@
+style: github
+template: CHANGELOG.tpl.md
+info:
+  title: CHANGELOG
+  repository_url: https://github.com/ge-high-assurance/RACK
+options:
+  commits:
+    # filters:
+    #   Type:
+    #     - feat
+    #     - fix
+    #     - perf
+    #     - refactor
+  commit_groups:
+    # title_maps:
+    #   feat: Features
+    #   fix: Bug Fixes
+    #   perf: Performance Improvements
+    #   refactor: Code Refactoring
+  header:
+    pattern: "^(\\w*)(?:\\(([\\w\\$\\.\\-\\*\\s]*)\\))?\\:\\s(.*)$"
+    pattern_maps:
+      - Type
+      - Scope
+      - Subject
+  notes:
+    keywords:
+      - BREAKING CHANGE
diff --git a/.github/workflows/actions/download/action.yml b/.github/workflows/actions/download/action.yml
@@ -24,7 +24,7 @@ runs:
 
     - name: Download SemTK distribution
       shell: bash
-      run: curl -LSfs https://github.com/ge-semtk/semtk/releases/download/v2.3.0-20201208/semtk-opensource-v2.3.0-20201208-dist.tar.gz -o RACK/rack-box/files/semtk.tar.gz
+      run: curl -LSfs https://github.com/ge-semtk/semtk/releases/download/v2.3.0-20210127/semtk-opensource-v2.3.0-20210127-dist.tar.gz -o RACK/rack-box/files/semtk.tar.gz
 
     - name: Download style spreadsheet
       shell: bash

diff --git a/.gitignore b/.gitignore
@@ -54,3 +54,4 @@ doc/internal
 
 TODO.org
 /.metadata/
+debug.log
diff --git a/Provenance-Example/Example.sadl b/Provenance-Example/Example.sadl
@@ -104,6 +104,7 @@ ExplanatoryRequirement
   is a REQUIREMENT
   createdBy DefineRequirements
   dataInsertedBy WriteSomeSadl
-  text "Help RACK users understand the difference between
+  description
+        "Help RACK users understand the difference between
         authorship of a requirement and the process of ingesting
         that requirement into RACK itself".
diff --git a/Provenance-Example/OwlModels/SadlBaseModel.owl b/Provenance-Example/OwlModels/SadlBaseModel.owl
@@ -0,0 +1,11 @@
+<rdf:RDF
+    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+    xmlns:owl="http://www.w3.org/2002/07/owl#"
+    xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+    xmlns:sadlbasemodel="http://sadl.org/sadlbasemodel#"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+  xml:base="http://sadl.org/sadlbasemodel">
+  <owl:Ontology rdf:about="">
+    <rdfs:comment xml:lang="en">Base model for SADL. These concepts can be used without importing.</rdfs:comment>
+  </owl:Ontology>
+</rdf:RDF>
diff --git a/Provenance-Example/OwlModels/SadlListModel.owl b/Provenance-Example/OwlModels/SadlListModel.owl
@@ -0,0 +1,32 @@
+<rdf:RDF
+    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+    xmlns:sadllistmodel="http://sadl.org/sadllistmodel#"
+    xmlns:owl="http://www.w3.org/2002/07/owl#"
+    xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+    xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+  xml:base="http://sadl.org/sadllistmodel">
+  <owl:Ontology rdf:about="">
+    <rdfs:comment xml:lang="en">Typed List model for SADL.</rdfs:comment>
+  </owl:Ontology>
+  <owl:Class rdf:ID="List"/>
+  <owl:ObjectProperty rdf:ID="rest">
+    <rdfs:range rdf:resource="#List"/>
+    <rdfs:domain rdf:resource="#List"/>
+  </owl:ObjectProperty>
+  <rdf:Property rdf:ID="first">
+    <rdfs:domain rdf:resource="#List"/>
+  </rdf:Property>
+  <owl:DatatypeProperty rdf:ID="maxLengthRestriction">
+    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#int"/>
+    <rdfs:domain rdf:resource="#List"/>
+  </owl:DatatypeProperty>
+  <owl:DatatypeProperty rdf:ID="lengthRestriction">
+    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#int"/>
+    <rdfs:domain rdf:resource="#List"/>
+  </owl:DatatypeProperty>
+  <owl:DatatypeProperty rdf:ID="minLengthRestriction">
+    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#int"/>
+    <rdfs:domain rdf:resource="#List"/>
+  </owl:DatatypeProperty>
+  <owl:AnnotationProperty rdf:ID="listtype"/>
+</rdf:RDF>