From 5a100045f632de98674ccecf4953160d391c173a Mon Sep 17 00:00:00 2001 From: Michael Hanke Date: Sun, 18 Feb 2024 09:21:02 +0100 Subject: [PATCH] Remove data access schema It was meant to be an explorative experiment, and I believe we have learned all we could. Time to let go. --- Makefile | 5 - .../ObjectAvailability-annexwebdav.json | 11 -- .../ObjectAvailability-annexwebdav.rdf | 10 -- .../ObjectAvailability-annexwebdav.yaml | 6 - src/extra-docs/data-access-schema/about.md | 0 src/extra-docs/index.md | 1 - src/linkml/schemas/data-access.yaml | 116 ------------------ .../GitAnnexSpecialRemote-missing_type.yaml | 8 -- .../validation/annexremote.valid.cfg.yaml | 8 -- .../annexremote_missing_type.invalid.cfg.yaml | 8 -- 10 files changed, 173 deletions(-) delete mode 100644 src/examples/data-access/ObjectAvailability-annexwebdav.json delete mode 100644 src/examples/data-access/ObjectAvailability-annexwebdav.rdf delete mode 100644 src/examples/data-access/ObjectAvailability-annexwebdav.yaml delete mode 100644 src/extra-docs/data-access-schema/about.md delete mode 100644 src/linkml/schemas/data-access.yaml delete mode 100644 tests/data-access-schema/validation/GitAnnexSpecialRemote-missing_type.yaml delete mode 100644 tests/data-access-schema/validation/annexremote.valid.cfg.yaml delete mode 100644 tests/data-access-schema/validation/annexremote_missing_type.invalid.cfg.yaml diff --git a/Makefile b/Makefile index 476f010..df32b01 100644 --- a/Makefile +++ b/Makefile @@ -23,7 +23,6 @@ build/context.jsonld: src/linkml/schemas/ontology.yaml build/linkml-docs: \ build/linkml-docs/ontology \ - build/linkml-docs/data-access \ build/linkml-docs/datalad-dataset-components \ build/linkml-docs/datalad-dataset-version # build/linkml-docs/git-provenance-schema @@ -49,7 +48,6 @@ check: check-models check-validation # add additional schemas to lint here check-models: \ - check-model-data-access \ check-model-datalad-dataset-components \ check-model-datalad-dataset-version \ check-model-ontology @@ -80,8 +78,6 @@ check-model-%: src/linkml/schemas/%.yaml # respective validation targets, because some tests rely on these # converted formats check-validation: \ - convert-examples-data-access \ - check-validation-data-access \ convert-examples-datalad-dataset-components \ check-validation-datalad-dataset-components \ convert-examples-datalad-dataset-version \ @@ -103,7 +99,6 @@ check-invalid-validation-%: tests/%-schema/validation src/linkml/schemas/%.yaml done convert-examples: \ - convert-examples-data-access \ convert-examples-datalad-dataset-components \ convert-examples-datalad-dataset-version \ convert-examples-ontology diff --git a/src/examples/data-access/ObjectAvailability-annexwebdav.json b/src/examples/data-access/ObjectAvailability-annexwebdav.json deleted file mode 100644 index c3efa97..0000000 --- a/src/examples/data-access/ObjectAvailability-annexwebdav.json +++ /dev/null @@ -1,11 +0,0 @@ -{ - "access_method": { - "meta_type": "dlco:GitAnnexSpecialRemote", - "special_remote_type": "webdav", - "has_parameter": [ - "some" - ] - }, - "object_id": "MD5E-s4--ba1f2511fc30423bdbb183fe33f3dd0f.txt", - "@type": "ObjectAvailability" -} diff --git a/src/examples/data-access/ObjectAvailability-annexwebdav.rdf b/src/examples/data-access/ObjectAvailability-annexwebdav.rdf deleted file mode 100644 index 4835612..0000000 --- a/src/examples/data-access/ObjectAvailability-annexwebdav.rdf +++ /dev/null @@ -1,10 +0,0 @@ -@prefix dlco: . -@prefix xsd: . - -[] a dlco:ObjectAvailability ; - dlco:access_method [ dlco:has_parameter "some" ; - dlco:meta_type "dlco:GitAnnexSpecialRemote"^^xsd:anyURI ; - dlco:special_remote_type "webdav" ] ; - dlco:object_id "MD5E-s4--ba1f2511fc30423bdbb183fe33f3dd0f.txt" . - - diff --git a/src/examples/data-access/ObjectAvailability-annexwebdav.yaml b/src/examples/data-access/ObjectAvailability-annexwebdav.yaml deleted file mode 100644 index c879603..0000000 --- a/src/examples/data-access/ObjectAvailability-annexwebdav.yaml +++ /dev/null @@ -1,6 +0,0 @@ -access_method: - meta_type: dlco:GitAnnexSpecialRemote - special_remote_type: webdav - has_parameter: - - some -object_id: MD5E-s4--ba1f2511fc30423bdbb183fe33f3dd0f.txt diff --git a/src/extra-docs/data-access-schema/about.md b/src/extra-docs/data-access-schema/about.md deleted file mode 100644 index e69de29..0000000 diff --git a/src/extra-docs/index.md b/src/extra-docs/index.md index afee2c2..c6f5475 100644 --- a/src/extra-docs/index.md +++ b/src/extra-docs/index.md @@ -1,5 +1,4 @@ - [DataLad concepts ontology](ontology/) - [DataLad dataset components schema](datalad-dataset-components-schema/) - [DataLad dataset version schema](datalad-dataset-version-schema/) -- [Data access schema](data-access-schema/) - [Git provenance schema](git-provenance-schema/) diff --git a/src/linkml/schemas/data-access.yaml b/src/linkml/schemas/data-access.yaml deleted file mode 100644 index ead0964..0000000 --- a/src/linkml/schemas/data-access.yaml +++ /dev/null @@ -1,116 +0,0 @@ -id: https://concepts.datalad.org/schemas/data-access -name: data-access-schema -title: Data access schema -description: >- - This is a schema draft centered around the annotation of availability of - objects. Such objects would typically be (or could become) the content - of a file. - This schema is not envisioned to be around for long, but it simply - smaller than a schema for describing complete datasets, hence simpler - to work with while exploring basic principles of data modeling. -prefixes: - dlco: https://concepts.datalad.org/ontology/ - schema: http://schema.org/ - linkml: https://w3id.org/linkml/ -imports: - - ../ontology/types - - ../ontology/meta_utils - - linkml:types -default_prefix: dlco - -slots: - has_parameter: - description: >- - Parameter of a system or algorithm. - - available_via: - description: >- - Method(s) through which an entity can be obtained. - related_mappings: - - schema:availableAtOrFrom - - access_method: - description: >- - Parametrizable method(s) through which objects can be obtained, - given an object identifier. - - object_id: - description: >- - (Alternative) identifier for an object (e.g., in a particular storage - system). - range: string - - -classes: - # technical vehicle for this schema and its validation - DataObject: - description: >- - Root object for this schema. not part of the ontology. - mixins: - - HasAvailability - - # TODO move to place for common mixins - HasAvailability: - mixin: true - description: >- - (Mixin) class for an object with an availability property. - slots: - - available_via - slot_usage: - available_via: - range: ObjectAvailability - multivalued: true - inlined: true - inlined_as_list: true - - ObjectAvailability: - description: >- - Record of availability of an object via an access method under a - particular identifier. - slots: - - access_method - - object_id - slot_usage: - access_method: - required: true - range: ObjectAccessMethod - inlined: true - object_id: - # not required, could be identical to an identifier in some other - # global context - required: false - - ObjectAccessMethod: - mixins: - - HasMetaTypeDesignator - description: >- - Parametrizable method through which objects can be obtained, - given an object identifier. - - # have this one as a "full" example - GitAnnexSpecialRemote: - is_a: ObjectAccessMethod - description: >- - Obtain an annex key object from a git-annex special remote. - attributes: - special_remote_type: - description: >- - Identifier of a git-annex special remote type. - For an external special remote implementation, this is - the remainder of the executable name that follows the - `git-annex-remote-` prefix. - required: true - range: string - slots: - - has_parameter - slot_usage: - has_parameter: - description: >- - Parameters to be given to `git annex initremote` in order to - initialize the remote. - range: string - multivalued: true - # the next two must not be used, unless range is a class definition - # and not just a type - #inlined: true - #inlined_as_list: true diff --git a/tests/data-access-schema/validation/GitAnnexSpecialRemote-missing_type.yaml b/tests/data-access-schema/validation/GitAnnexSpecialRemote-missing_type.yaml deleted file mode 100644 index f89d734..0000000 --- a/tests/data-access-schema/validation/GitAnnexSpecialRemote-missing_type.yaml +++ /dev/null @@ -1,8 +0,0 @@ -available_via: - - access_method: - meta_type: GitAnnexSpecialRemote - # special_remote_type is required - #special_remote_type: webdav - has_parameter: - - some - - object_id: MD5E-s4--ba1f2511fc30423bdbb183fe33f3dd0f.txt diff --git a/tests/data-access-schema/validation/annexremote.valid.cfg.yaml b/tests/data-access-schema/validation/annexremote.valid.cfg.yaml deleted file mode 100644 index c747d5d..0000000 --- a/tests/data-access-schema/validation/annexremote.valid.cfg.yaml +++ /dev/null @@ -1,8 +0,0 @@ -schema: src/linkml/schemas/data-access.yaml -target_class: ObjectAvailability -data_sources: - - src/examples/data-access/ObjectAvailability-annexwebdav.yaml -plugins: - JsonschemaValidationPlugin: - closed: true - RecommendedSlotsPlugin: diff --git a/tests/data-access-schema/validation/annexremote_missing_type.invalid.cfg.yaml b/tests/data-access-schema/validation/annexremote_missing_type.invalid.cfg.yaml deleted file mode 100644 index 1b2605b..0000000 --- a/tests/data-access-schema/validation/annexremote_missing_type.invalid.cfg.yaml +++ /dev/null @@ -1,8 +0,0 @@ -schema: src/linkml/schemas/data-access.yaml -target_class: DataObject -data_sources: - - tests/data-access-schema/validation/GitAnnexSpecialRemote-missing_type.yaml -plugins: - JsonschemaValidationPlugin: - closed: true - RecommendedSlotsPlugin: