Arango-rdf

Other

* Update README.md. [Anthony Mahanna]

* Fix broken readme link. [Anthony Mahanna]

Other

* Fix hyperlinks. [Anthony Mahanna]

* Documentation updates (19) [Anthony Mahanna]

* cleanup hash logic, make `rdf_graph` private

* checkpoint

* more cleanup

* update action versions

* checkpoint

* update tests

* checkpoint: green tests

* checkpoint: cases `14_2` and `15` are failing

* fix: make `__hash()` public

* cleanup `conftest`

* fix `v_count/e_count` assertions, more test cleanup

* new: case 15_1, 15_2, 15_3

* cleanup case 13

* checkpoing: all tests green (except 1 flaky)

15_2 RPT is flaky, need to revisit

* update case 14_1

* cleanup tests

* checkpoint: `__process_subject_predicate_object`

* fix lint

* fix conftest

* set `continue-on-error`

* update case `15_2` (still flaky)

* fix: `type` instead of `isinstance`

* update case `14_1`

* update tests

* update case `container.ttl`

* update `test_main`

add `+ RDFGraph()` hack, update `test_pgt_container`

* new: `pgt_remove_blacklisted_statements`, `pgt_parse_literal_statements`, remove `adb_col_blacklist`

so many todos...

* fix flake

* new: case 13_1 and 13_2

* new: case 14_3

* new: case 15_4

* update tests

* fix: rdf namespacing

* fix case 7 and native graph

* new: `adb_col_statements`, `write_adb_col_statements` (pgt)

* update 13_2, 15_2, 14_3

* new test cases, use `pytest.xfail` on flaky assertions

tests should be green now...

* flake ignore

can't reproduce

* new: `explicit_metagraph`, optimize `fetch_adb_docs`

* fix typo

* cleanup: `**adb_kwargs`

* doc cleanup

* cleanup

* cleanup: `flatten_reified_triples`

* cleanup: progress/spinner bars via `rich`

* more `rich` cleanup

* update cases 10, 14.3, 15_4

* final main checkpoint: `arango_rdf`

* minor cleanup

* new: `__pgt_process_rdf_literal`

* new: `serialize` as a conversion mode

* new: `test_open_intelligence_graph`

* fix lint

* fix: `statements`, `rdf_graph` ref

* cleanup: `write_adb_col_statements`

* initial commit

* fix lint

* update notebook

* checkpoint

* fix lint

* Create .readthedocs.yaml

* Update README.md

* Update requirements.txt

* fix: code block warning

* cleanup

* nit

* fix hyperlinks

* fix docstring

* Housekeeping (18) [Anthony Mahanna]

* cleanup hash logic, make `rdf_graph` private

* checkpoint

* more cleanup

* update action versions

* checkpoint

* update tests

* checkpoint: green tests

* checkpoint: cases `14_2` and `15` are failing

* fix: make `__hash()` public

* cleanup `conftest`

* fix `v_count/e_count` assertions, more test cleanup

* new: case 15_1, 15_2, 15_3

* cleanup case 13

* checkpoing: all tests green (except 1 flaky)

15_2 RPT is flaky, need to revisit

* update case 14_1

* cleanup tests

* checkpoint: `__process_subject_predicate_object`

* fix lint

* fix conftest

* set `continue-on-error`

* update case `15_2` (still flaky)

* fix: `type` instead of `isinstance`

* update case `14_1`

* update tests

* update case `container.ttl`

* update `test_main`

add `+ RDFGraph()` hack, update `test_pgt_container`

* new: `pgt_remove_blacklisted_statements`, `pgt_parse_literal_statements`, remove `adb_col_blacklist`

so many todos...

* fix flake

* new: case 13_1 and 13_2

* new: case 14_3

* new: case 15_4

* update tests

* fix: rdf namespacing

* fix case 7 and native graph

* new: `adb_col_statements`, `write_adb_col_statements` (pgt)

* update 13_2, 15_2, 14_3

* new test cases, use `pytest.xfail` on flaky assertions

tests should be green now...

* flake ignore

can't reproduce

* new: `explicit_metagraph`, optimize `fetch_adb_docs`

* fix typo

* cleanup: `**adb_kwargs`

* doc cleanup

* cleanup

* cleanup: `flatten_reified_triples`

* cleanup: progress/spinner bars via `rich`

* more `rich` cleanup

* update cases 10, 14.3, 15_4

* final main checkpoint: `arango_rdf`

* minor cleanup

* new: `__pgt_process_rdf_literal`

* new: `serialize` as a conversion mode

* new: `test_open_intelligence_graph`

* fix lint

* fix: `statements`, `rdf_graph` ref

* cleanup: `write_adb_col_statements`

* Revert 6f85c04. [Anthony Mahanna]

* Cleanup: notebooks. [Anthony Mahanna]

* Update notebook output. [Anthony Mahanna]

* Fix pepy badge. [Anthony Mahanna]

Other

* ArangoRDF Overhaul: 0.1.0 (15) [Anthony Mahanna]

* new: test suite & test data

* update: repo config

* new: arango_rdf overhaul checkpoint

* temp: base ontology files

location TBD

* new: `flake8` & `mypy` workflows

* fix: black, flake, mypy

* cleanup

* temp: disable black worflow

* fix: add flake & mypy dependency

* fix: add `rich` dependency

* temp: disable `mypy` workflow

getting inconsistent `mypy` results between local environment & Github Actions environment

* enable: black, mypy

* cleanup: `arango_rdf`

formatting fixes, mypy fixes, docstring updates, general code cleanup

* black: test_main

* update: setup files

* update: test_pgt_case_3_2

addresses all **list_conversion** parameter cases

* update: tests

* misc: pragma no cover

* fix: test assertions

* update: test_rpt_basic_cases

* cleanup: main

* new: `rich` Live Group progress bars, `batch_size` parameter, code cleanup

* update: `rich` trackers in utils

* new: `RDFLists` typing

* new: ignore E266 flake8

* misc: line breaks

* update: `process_rpt_term`, pragma no cover

* new: case 7 prototype

* update 6.trig

* cleanup utils

* cleanup

* variable renaming, cleanup

* cleanup: test data

* rework: test suite

* remove: examples/data

* remove: arango_rdf/ontologies

* new: arango_rdf/meta

* checkpoint: arango_rdf

* fix: isort

* fix: compare_graphs

* temp fix: mypy

* new: fraud detection & imdb tests

* checkpoint: main.py

* fix: isort

* fix: isort (again)

* new: meta files

switching to `trig` format

* checkpoint: tests

* checkpoint: arango_rdf

working on adb mapping functionality

* checkpoint: tests

* checkpoint: arango_rdf

* cleanup: tests

* checkpoint: arango_rdf

* update: test cases

* cleanup: arango_rdf

* fix: rpt case 5

* cleanup: tests

* new: cityhash dependency

* cleanup & docstrings: arango_rdf

flake8 will fail

* fix: flake8

autopep8 & yapf did not work, manual fix was required

* fix: pgt case 6

* new: __build_subclass_tree() and __identify_best_class()

* update: Tree.show()

* cleanup main

* new: dc.trig & xsd.trig starter files

only adding the nodes that are referenced by the other ontologies (OWL, RDF, RDFS) for now

* update: tests

* cleanup: arango_rdf

new `__pgt_add_to_adb_mapping` helper method, add restriction to property type relationship creation if contextualize_graph = True

* fix: pgt case 2_4

* more cleanup: arango_rdf

* new: load RDF Predicates regardless of contextualize_graph value (PGT only)

* update: test_adb_native_graph_to_rdf

* attempt fix: missing coverage on L922

coveralls seems to think this line is not covered by tests...

* Update README.md

* update docstrings

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* fix: flake8

* Update README.md

* new: notebook overhaul baseline

* fix: process_val_as_string

* remove: unused func

* fix: p_already_has_dr

* new: __get_literal_val

* update: __get_literal_val

* fix: subgraph names

* cp: adb_key_uri

* cleanup: arango_rdf

* update: meta trig files

* cleanup: arango_rdf

* update: tests

* more cleanup

* fix: flake8

* new: ArangoRDFController

* fix: isort

* new: use_async (rdf to arangodb)

* cleanup

* update test params

* update: test case 7

* cleanup: insert_adb_docs

* update: tests

* cleanup

* new: ArangoRDF.ipynb output file

* revert: d2277fa7f66a04d148b23ce04d9ad92db598f97c

* new: game of thrones dump

* update: tests

* cp: arango_rdf

* update notebook

* new: cases 8-15 in notebook

* new: rdf-star support for rpt

* Revert "new: rdf-star support for rpt"

This reverts commit 2a0ae04c445ba21f254de7927375a771b43abd65.

* checkpoint

rdf-star support prototyping,

* cleanup: adb to rdf

* new: rdf_statement_blacklist

* discard "List" collection for pgt

* new: __get_adb_edge_key

* cleanup

* checkpoint

* cleanup

* new: rdf star cases (8 to 15)

* new: individualize RPT tests

* Update ArangoRDF.ipynb

* cleanup

* new: hash adb edge ids

* update: rdf-star support workaround

* new: test cases 8-15 (pgt)

* update notebook

* cleanup

* actions: use ArangoDB 3.11

* fix notebook

* cleanup

* Update setup.py

* new: design doc

template used: https://github.com/arangodb/documents/blob/master/DesignDocuments/DesignDocumentTemplate.md

* new: simplify_reified_triples flag

* new: keyify_literals (rpt)

minor cleanup

* rework: batch_size (adb to rdf)

* use batch_size in tests

(adb to rdf & rdf to adb)

* new: adb_key URI test case

* cleanup based on feedback

* fix: mypy

* update build workflow

* update release workflow

* cleanup, todo comments

* swap python 3.7 for 3.12

* cleanup tests (case 1 & 6)

* cleanup

* migrate to `pyproject.toml`

* fix lint

* fix mypy

* flake8 extend ignore

trying to workaround 3.12 builds: https://github.com/ArangoDB-Community/ArangoRDF/actions/runs/6856708733/job/18644393745?pr=15

* Update ArangoRDF.ipynb. [Chris Woodward]

Removes expected time message as it is much faster now

New

* Test suite, repo config updates, CICD via Actions (9) [Anthony Mahanna]

* new: pytest suite

note: `test_full_cycle_aircraft_without_normalize_literals` is currently failing

* new: tqdm progress bar, cleanup export, set `import_ontology` as out of service

* new: CICD via Github Actions

CodeQL, test automation, release automation

* new: config files

* remove: import_ontology

* fix: rename `export` to `export_rdf`

* fix: actions branch target

* update: ground truth for test_main

* cleanup: main.py

housekeeping, refactoring, new helper methods, etc.

* remove: init_ontology_collections

references 6

* Update .gitignore

* remove: round timestamp

* Update test_main.py

* rename: export_rdf

* Update README.md

* Update README.md

* new: README badges

Other

* Fix typo. [Chris Woodward]

* Update ArangoRDF_output.ipynb. [Chris Woodward]

Update branch name

* Update ArangoRDF.ipynb. [Chris Woodward]

update branch name

* Example update (7) [Chris Woodward]

* adds new example data, updates README example, adds note about ontology issues

* small README fixes, adds notebook

* black formatting

* Update README.md. [Chris Woodward]

Fixes example code to match recent codebase changes

* Update setup.py. [aMahanna]

* Update README.md. [aMahanna]

New

* Codebase cleanup (5) [Anthony Mahanna]

What's new:

- Codebase housekeeping
- README updates
- new: custom Configurations
- new: normalize literals functionality
- new: default_graph and sub_graph properties in constructor

All changes were discussed and reviewed with ArthurKeen and cw00dw0rd

New

* Constructor cleanup (4) [Anthony Mahanna]

Other

* Update MANIFEST.in. [aMahanna]

* Update README.md. [Chris Woodward]

* Initial Merge (1) [Chris Woodward]

* initial commit for topology preserving rdf import

* added test data and file. also added s to arangoSemantics

* removed file with old name

* added ontology import method

* modified test.py file to test both target variants. added a metadata.ttl file containing rdf/rdfs/owl/skos metamodels

* Added code to test the loading of the RDFS/OWL/SKOS metadata, added condition to add xsd:string as a type to string without a type

* separate rdfowl and skos in metadata folder and tested

* added method for exporting to a file

* cleaned up test.py

* cleaned up code and added doc strings

* ArangoRDF Refactoring (2)

* initial refactoring

project structuring, code formatting, basic test suite, README, setup.py, etc.

* delete: rdfExport.ttl

* Update ArangoRDF.ipynb

* new: utf8 encoding

* Update README.md

* update to localhost

* new: code authors

* Update setup.py

* Initial commit. [Chris Woodward]