Release 0.8.0 #79
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Release 0.8.0 #79
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Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
Release 0.7.0
Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
Fix homepage link
Regenerating due to a local tool update. Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
This also updates the submodules to catch their updated `case-utils`
adoption status.
This patch also incorporates packages required for testing by making a
`testing` feature for `case_prov`, that only depends on `case_utils`'
`testing` feature, without a version description. This was confirmed to
respect the version restrictions in `install_requires` by trying this
configuration and seeing it fail to find the `testing` feature
introduced in `case-utils 0.11.0`:
```
[options]
install_requires =
case_utils >=0.10.0,< 0.11.0
[options.extras_require]
testing=
case_utils[testing]
```
No effects were observed on Make-managed files.
Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
Bump case-utils adoption to 0.11.0
No effects were observed on Make-managed files. Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
References: * https://www.w3.org/TR/owl-time/#fig-thirteen-elementary-possible-relations-between-time-periods-af-97 Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
No effects were observed on Make-managed files. Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
Fix Association query typo
…nodes This patch uses the inherence UUID functions from `case-utils` PR 112 to replace the blank nodes generated with SPARQL Construct queries. As side effects of this migration, some bugs were fixed with generating some associations, and inherence modeling assumptions are now specified in code comments. This patch also adds `prov:Start` and `prov:End` nodes to reify `prov:Activity` (and `case-investigation:InvestigativeAction`) time boundaries. This will be a significant assistance in OWL-Time-based visualization under development for `case-prov` PR 54. Creating the `prov:Start` and `prov:End` nodes as IRI-identified is also necessary because of a bug observed in `rdf-toolkit`; see their Issue 52. Since `case_prov_rdf` will now be able to generate non-blank nodes, it has picked up two behaviors used in other projects importing `case-utils`: * The `--use-deterministic-uuids` flag has been added. * The `CASE_DEMO_NONRANDOM_UUID_BASE` environment variable can now be used to make non-inherent deterministic UUIDs. A follow-on patch will regenerate Make-managed files. References: * #54 * casework/CASE-Utilities-Python#112 * edmcouncil/rdf-toolkit#52 Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
Use inherent IDs to infer qualified Influence and InstantaneousEvent nodes
This patch fixes a bug based on an implementation pattern. Currently, SPARQL queries that can potentially return multiple results (e.g. due to multiple RDFS Comments) only build the PyDot Node label based on the last query result returned. This leads to dropped annotations as well as potentially non-deterministic behavior (especially from the lack of sorting). This patch's implementation is mainly code motion. It also starts moving the RDF logistics more towards RDF types rather than collapsing types into strings. (RDFLib type review support was in a much earlier implementation state when this code was first written.) This patch will induce slight lateral motion in Activity nodes, due to a leading whitespace character on the time-interval line being removed. A follow-on patch will regenerate Make-managed files. Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
This patch adapts the forward-porting pattern done for `case-investigation:exhibitNumber`, carrying forward `uco-core:name` and `uco-core:description` in the generated PROV-O triples. In cases where the triples are folded back into the input graph, the changes to the `CONSTRUCT` queries will have no effect. With `name` and `description` brought forward, instead of being collapsed into `rdfs:comment`s, their order (as groups of annotations) can be controlled in rendered node labels. The general order is now: * Name * Label(s) * Description(s) * Comment(s) A follow-on patch will regenerate Make-managed files. Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
This patch is code motion, moving some function calls to their needed time of calling at the end of the rendering process. No effects were observed on Make-managed files. Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
Reduce edge construction
This patch is code motion, moving some function calls to their needed time of calling at the end of the rendering process. No effects were observed on Make-managed files. Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
Reduce node construction
Forward UCO names and descriptions
This patch revises `case_prov_dot` to make use of updates in code review practice and upstream typing support since the script was originally written. The original version of `case_prov_dot` relied on many conversions of RDFLib types to strings. This induced some reinvention of logical organization of concepts into IRI strings vs. quickly-instantiated and -discarded `rdflib.URIRef` objects. Some usage of `URIRef`s as strings was covered by `URIRef`s being implemented in RDFLib as subclasses of string. As work progressed on adding TIME concept support (see PR 54), it became unnecessarily burdensome to handle some work with managing untyped strings under specialized consideration, versus constructing sets of `rdflib.URIRef`s to designate nodes. Managing potential blank nodes also became a challenge with casts to strings. This patch revises the base work in `case_prov_dot` to be oriented on analyzing sets of `rdflib.term.IdentifiedNode`s (encompassing `URIRef`s and `BNode`s). A roadmap/codemap is also added in inline documentation to describe sections of code behavior. Revision of the code flow also settled some design issues that were previously unnecessarily isolating the various chains from one another, especially where some chains needed to be handled as a mutual union, and another needed to be handled as an intersection, when various subsets of the provenance graph are requested. So this patch also adds the various pairs of chains as demonstrations under the Urgent Evidence example. A follow-on patch will regenerate Make-managed files. References: * #54 Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
Re-flow case_prov_dot
This merge re-applied changes done for `case_prov_dot.py`, with some fixes applied for issues reported by `mypy`. No effects were observed on Make-managed files.
No effects were observed on Make-managed files. Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
This figure shows only two of the Allen interval-relations are handled by the ordering logic now. However, the figure does show time flowing "downward" by seeing the before & after `*-i` intervals are above the `*-j` intervals. A follow-on patch will regenerate Make-managed files. Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
Review with mypy --strict
This patch enables `pytest`'s doctest mode and adds a first doctest to ensure `pytest` doesn't fail due to finding no tests to run. Follow-on patches will add new functions with more demanding doctests. No effects were observed on Make-managed files. References: * https://docs.pytest.org/en/7.1.x/how-to/doctest.html * casework/CASE-Utilities-Python#111 Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
This function is added independently, without usage yet, to isolate test effects. No effects were observed on Make-managed files. Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
This function is added independently, without usage yet, to isolate test effects. No effects were observed on Make-managed files. Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
This patch adds inferential analysis to define temporal interval boundaries and apply timeline sorting, both topologically and lexicographically. CASE Investigative Actions are already inferred by current `case_prov_rdf` and `case_prov_dot` practice to be PROV Activities. This patch takes inference further to interpret PROV Activities as OWL-Time Proper Intervals. Further, PROV Instantaneous Events are inferred to be OWL-Time Instants, and their relationships to Entities and Activities are used to establish topological order according to PROV (English) definitions. All OWL-Time Instants, and nodes inferred to be OWL-Time Instants, are assigned `xsd:dateTimeStamp` values in GMT (where possible) to enable a timeline based on lexicographic sorting. Figures' and tests' Makefiles are updated to add new graphs to display. A follow-on patch will regenerate Make-managed files, and track new figures. The last planned follow-on patch will add OWL-Time documentation to the top README. Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
A follow-on patch will regenerate Make-managed files. The patch afterwards will add OWL-Time documentation to the top README. Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
The RDFLib issue referenced in the comment summarizes the type-safety matter. No effects were observed on Make-managed files. Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
Use any existing TIME hints in graph to do further ordering.
This is only a refresh to the current pointer. No effects were observed on Make-managed files. Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
kchason
approved these changes
Jun 12, 2023
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