diff --git a/nwb-schema-linkml/.cruft.json b/nwb-schema-language/.cruft.json similarity index 100% rename from nwb-schema-linkml/.cruft.json rename to nwb-schema-language/.cruft.json diff --git a/nwb-schema-linkml/.github/workflows/deploy-docs.yaml b/nwb-schema-language/.github/workflows/deploy-docs.yaml similarity index 100% rename from nwb-schema-linkml/.github/workflows/deploy-docs.yaml rename to nwb-schema-language/.github/workflows/deploy-docs.yaml diff --git a/nwb-schema-linkml/.github/workflows/main.yaml b/nwb-schema-language/.github/workflows/main.yaml similarity index 100% rename from nwb-schema-linkml/.github/workflows/main.yaml rename to nwb-schema-language/.github/workflows/main.yaml diff --git a/nwb-schema-linkml/.github/workflows/pypi-publish.yaml b/nwb-schema-language/.github/workflows/pypi-publish.yaml similarity index 100% rename from nwb-schema-linkml/.github/workflows/pypi-publish.yaml rename to nwb-schema-language/.github/workflows/pypi-publish.yaml diff --git a/nwb-schema-linkml/.gitignore b/nwb-schema-language/.gitignore similarity index 100% rename from nwb-schema-linkml/.gitignore rename to nwb-schema-language/.gitignore diff --git a/nwb-schema-linkml/CODE_OF_CONDUCT.md b/nwb-schema-language/CODE_OF_CONDUCT.md similarity index 100% rename from nwb-schema-linkml/CODE_OF_CONDUCT.md rename to nwb-schema-language/CODE_OF_CONDUCT.md diff --git a/nwb-schema-linkml/CONTRIBUTING.md b/nwb-schema-language/CONTRIBUTING.md similarity index 100% rename from nwb-schema-linkml/CONTRIBUTING.md rename to nwb-schema-language/CONTRIBUTING.md diff --git a/nwb-schema-linkml/LICENSE b/nwb-schema-language/LICENSE similarity index 100% rename from nwb-schema-linkml/LICENSE rename to nwb-schema-language/LICENSE diff --git a/nwb-schema-linkml/Makefile b/nwb-schema-language/Makefile similarity index 97% rename from nwb-schema-linkml/Makefile rename to nwb-schema-language/Makefile index 88f65f3..0d69d5f 100644 --- a/nwb-schema-linkml/Makefile +++ b/nwb-schema-language/Makefile @@ -106,6 +106,8 @@ gen-examples: gen-project: $(PYMODEL) $(RUN) gen-project ${GEN_PARGS} -d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL) +gen-pydantic: $(PYMODEL) + $(RUN) gen-pydantic $(SOURCE_SCHEMA_PATH) --pydantic_version 1 > $(PYMODEL)/nwb_schema_pydantic.py test: test-schema test-python test-examples diff --git a/nwb-schema-linkml/README.md b/nwb-schema-language/README.md similarity index 100% rename from nwb-schema-linkml/README.md rename to nwb-schema-language/README.md diff --git a/nwb-schema-linkml/about.yaml b/nwb-schema-language/about.yaml similarity index 66% rename from nwb-schema-linkml/about.yaml rename to nwb-schema-language/about.yaml index 6a10bbe..83154a8 100644 --- a/nwb-schema-linkml/about.yaml +++ b/nwb-schema-language/about.yaml @@ -3,5 +3,5 @@ name: nwb_schema_language author: Jonny Saunders description: Translation of the nwb-schema-language to LinkML source_schema_path: src/nwb_schema_language/schema/nwb_schema_language.yaml -google_sheet_id: 1wVoaiFg47aT9YWNeRfTZ8tYHN8s8PAuDx5i2HUcDpvQ -google_sheet_tabs: personinfo enums +#google_sheet_id: 1wVoaiFg47aT9YWNeRfTZ8tYHN8s8PAuDx5i2HUcDpvQ +#google_sheet_tabs: personinfo enums diff --git a/nwb-schema-linkml/config.env b/nwb-schema-language/config.env similarity index 100% rename from nwb-schema-linkml/config.env rename to nwb-schema-language/config.env diff --git a/nwb-schema-linkml/config.yaml b/nwb-schema-language/config.yaml similarity index 95% rename from nwb-schema-linkml/config.yaml rename to nwb-schema-language/config.yaml index 56da66d..73c0387 100644 --- a/nwb-schema-linkml/config.yaml +++ b/nwb-schema-language/config.yaml @@ -24,6 +24,8 @@ generator_args: mergeimports: true python: mergeimports: true + pydantic: + mergeimports: true prefixmap: mergeimports: true proto: diff --git a/nwb-schema-linkml/mkdocs.yml b/nwb-schema-language/mkdocs.yml similarity index 100% rename from nwb-schema-linkml/mkdocs.yml rename to nwb-schema-language/mkdocs.yml diff --git a/nwb-schema-linkml/poetry.lock b/nwb-schema-language/poetry.lock similarity index 100% rename from nwb-schema-linkml/poetry.lock rename to nwb-schema-language/poetry.lock diff --git a/nwb-schema-linkml/project.Makefile b/nwb-schema-language/project.Makefile similarity index 100% rename from nwb-schema-linkml/project.Makefile rename to nwb-schema-language/project.Makefile diff --git a/nwb-schema-language/project/excel/nwb_schema_language.xlsx b/nwb-schema-language/project/excel/nwb_schema_language.xlsx new file mode 100644 index 0000000..fcd7b40 Binary files /dev/null and b/nwb-schema-language/project/excel/nwb_schema_language.xlsx differ diff --git a/nwb-schema-linkml/project/graphql/nwb_schema_language.graphql b/nwb-schema-language/project/graphql/nwb_schema_language.graphql similarity index 93% rename from nwb-schema-linkml/project/graphql/nwb_schema_language.graphql rename to nwb-schema-language/project/graphql/nwb_schema_language.graphql index ad4088e..9b1ef09 100644 --- a/nwb-schema-linkml/project/graphql/nwb_schema_language.graphql +++ b/nwb-schema-language/project/graphql/nwb_schema_language.graphql @@ -38,6 +38,11 @@ type Dataset implements DtypeMixin, NamingMixin dtype: String } +type Datasets + { + datasets: [Dataset] + } + interface DtypeMixin { dtype: String @@ -58,6 +63,11 @@ type Group implements NamingMixin links: [Link] } +type Groups + { + groups: [Group] + } + type Link { name: String @@ -97,8 +107,8 @@ type Schema { source: String namespace: String - doc: String! title: String neurodataTypes: [String] + doc: String } diff --git a/nwb-schema-linkml/project/jsonld/nwb_schema_language.context.jsonld b/nwb-schema-language/project/jsonld/nwb_schema_language.context.jsonld similarity index 96% rename from nwb-schema-linkml/project/jsonld/nwb_schema_language.context.jsonld rename to nwb-schema-language/project/jsonld/nwb_schema_language.context.jsonld index bf2df2b..82d7b9e 100644 --- a/nwb-schema-linkml/project/jsonld/nwb_schema_language.context.jsonld +++ b/nwb-schema-language/project/jsonld/nwb_schema_language.context.jsonld @@ -1,7 +1,7 @@ { "comments": { "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-16T23:21:36", + "generation_date": "2023-08-18T00:36:53", "source": "nwb_schema_language.yaml" }, "@context": { diff --git a/nwb-schema-linkml/project/jsonld/nwb_schema_language.jsonld b/nwb-schema-language/project/jsonld/nwb_schema_language.jsonld similarity index 97% rename from nwb-schema-linkml/project/jsonld/nwb_schema_language.jsonld rename to nwb-schema-language/project/jsonld/nwb_schema_language.jsonld index 877cc8e..5d62f63 100644 --- a/nwb-schema-linkml/project/jsonld/nwb_schema_language.jsonld +++ b/nwb-schema-language/project/jsonld/nwb_schema_language.jsonld @@ -457,7 +457,6 @@ "owner": "CompoundDtype", "domain_of": [ "Namespace", - "Schema", "Group", "Attribute", "Link", @@ -635,6 +634,7 @@ ], "range": "Namespace", "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -791,12 +791,14 @@ "from_schema": "https://w3id.org/p2p_ld/nwb-schema-language", "slot_uri": "https://w3id.org/p2p_ld/nwb-schema-language/datasets", "multivalued": true, - "owner": "Group", + "owner": "Datasets", "domain_of": [ - "Group" + "Group", + "Datasets" ], "range": "Dataset", "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -805,12 +807,14 @@ "from_schema": "https://w3id.org/p2p_ld/nwb-schema-language", "slot_uri": "https://w3id.org/p2p_ld/nwb-schema-language/groups", "multivalued": true, - "owner": "Group", + "owner": "Groups", "domain_of": [ - "Group" + "Group", + "Groups" ], "range": "Group", "inlined": true, + "inlined_as_list": true, "@type": "SlotDefinition" }, { @@ -838,7 +842,7 @@ "DtypeMixin" ], "range": "string", - "exactly_one_of": [ + "any_of": [ { "range": "FlatDtype", "@type": "AnonymousSlotExpression" @@ -981,6 +985,18 @@ "range": "reftype_options", "@type": "SlotDefinition" }, + { + "name": "schema__doc", + "from_schema": "https://w3id.org/p2p_ld/nwb-schema-language", + "slot_uri": "https://w3id.org/p2p_ld/nwb-schema-language/doc", + "alias": "doc", + "owner": "Schema", + "domain_of": [ + "Schema" + ], + "range": "string", + "@type": "SlotDefinition" + }, { "name": "Namespace_name", "definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/name", @@ -1004,25 +1020,6 @@ }, "@type": "SlotDefinition" }, - { - "name": "Schema_doc", - "definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/doc", - "description": "Description of corresponding object.", - "from_schema": "https://w3id.org/p2p_ld/nwb-schema-language", - "is_a": "doc", - "domain": "Schema", - "slot_uri": "https://w3id.org/p2p_ld/nwb-schema-language/doc", - "alias": "doc", - "owner": "Schema", - "domain_of": [ - "Schema" - ], - "is_usage_slot": true, - "usage_slot_name": "doc", - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, { "name": "Attribute_name", "definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/name", @@ -1085,7 +1082,7 @@ "usage_slot_name": "dtype", "range": "FlatDtype", "required": true, - "exactly_one_of": [ + "any_of": [ { "range": "FlatDtype", "@type": "AnonymousSlotExpression" @@ -1139,11 +1136,17 @@ "slots": [ "source", "namespace", - "Schema_doc", "title", - "neurodata_types" + "neurodata_types", + "schema__doc" ], "slot_usage": {}, + "attributes": [ + { + "name": "doc", + "@type": "SlotDefinition" + } + ], "class_uri": "https://w3id.org/p2p_ld/nwb-schema-language/Schema", "rules": [ { @@ -1287,6 +1290,17 @@ "class_uri": "https://w3id.org/p2p_ld/nwb-schema-language/Group", "@type": "ClassDefinition" }, + { + "name": "Groups", + "definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/Groups", + "from_schema": "https://w3id.org/p2p_ld/nwb-schema-language", + "slots": [ + "groups" + ], + "slot_usage": {}, + "class_uri": "https://w3id.org/p2p_ld/nwb-schema-language/Groups", + "@type": "ClassDefinition" + }, { "name": "Attribute", "definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/Attribute", @@ -1349,6 +1363,17 @@ "class_uri": "https://w3id.org/p2p_ld/nwb-schema-language/Dataset", "@type": "ClassDefinition" }, + { + "name": "Datasets", + "definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/Datasets", + "from_schema": "https://w3id.org/p2p_ld/nwb-schema-language", + "slots": [ + "datasets" + ], + "slot_usage": {}, + "class_uri": "https://w3id.org/p2p_ld/nwb-schema-language/Datasets", + "@type": "ClassDefinition" + }, { "name": "ReferenceDtype", "definition_uri": "https://w3id.org/p2p_ld/nwb-schema-language/ReferenceDtype", @@ -1491,9 +1516,9 @@ ], "metamodel_version": "1.7.0", "source_file": "nwb_schema_language.yaml", - "source_file_date": "2023-08-16T23:21:07", - "source_file_size": 10816, - "generation_date": "2023-08-16T23:21:36", + "source_file_date": "2023-08-18T00:28:45", + "source_file_size": 10952, + "generation_date": "2023-08-18T00:36:53", "settings": [ { "setting_key": "email", diff --git a/nwb-schema-linkml/project/jsonschema/nwb_schema_language.schema.json b/nwb-schema-language/project/jsonschema/nwb_schema_language.schema.json similarity index 95% rename from nwb-schema-linkml/project/jsonschema/nwb_schema_language.schema.json rename to nwb-schema-language/project/jsonschema/nwb_schema_language.schema.json index 61674ad..b0e99b5 100644 --- a/nwb-schema-linkml/project/jsonschema/nwb_schema_language.schema.json +++ b/nwb-schema-language/project/jsonschema/nwb_schema_language.schema.json @@ -25,7 +25,7 @@ "type": "string" }, "dtype": { - "oneOf": [ + "anyOf": [ { "$ref": "#/$defs/FlatDtype" }, @@ -123,7 +123,7 @@ "type": "string" }, "dtype": { - "oneOf": [ + "anyOf": [ { "$ref": "#/$defs/FlatDtype" }, @@ -186,6 +186,20 @@ "title": "Dataset", "type": "object" }, + "Datasets": { + "additionalProperties": false, + "description": "", + "properties": { + "datasets": { + "items": { + "$ref": "#/$defs/Dataset" + }, + "type": "array" + } + }, + "title": "Datasets", + "type": "object" + }, "FlatDtype": { "description": "", "enum": [ @@ -283,6 +297,20 @@ "title": "Group", "type": "object" }, + "Groups": { + "additionalProperties": false, + "description": "", + "properties": { + "groups": { + "items": { + "$ref": "#/$defs/Group" + }, + "type": "array" + } + }, + "title": "Groups", + "type": "object" + }, "Link": { "additionalProperties": false, "description": "", @@ -526,7 +554,6 @@ "description": "", "properties": { "doc": { - "description": "Description of corresponding object.", "type": "string" }, "namespace": { diff --git a/nwb-schema-linkml/project/owl/nwb_schema_language.owl.ttl b/nwb-schema-language/project/owl/nwb_schema_language.owl.ttl similarity index 100% rename from nwb-schema-linkml/project/owl/nwb_schema_language.owl.ttl rename to nwb-schema-language/project/owl/nwb_schema_language.owl.ttl diff --git a/nwb-schema-linkml/project/prefixmap/nwb_schema_language.yaml b/nwb-schema-language/project/prefixmap/nwb_schema_language.yaml similarity index 100% rename from nwb-schema-linkml/project/prefixmap/nwb_schema_language.yaml rename to nwb-schema-language/project/prefixmap/nwb_schema_language.yaml diff --git a/nwb-schema-linkml/project/protobuf/nwb_schema_language.proto b/nwb-schema-language/project/protobuf/nwb_schema_language.proto similarity index 93% rename from nwb-schema-linkml/project/protobuf/nwb_schema_language.proto rename to nwb-schema-language/project/protobuf/nwb_schema_language.proto index a420081..d83b54b 100644 --- a/nwb-schema-linkml/project/protobuf/nwb_schema_language.proto +++ b/nwb-schema-language/project/protobuf/nwb_schema_language.proto @@ -31,6 +31,10 @@ message Dataset repeated attribute attributes = 0 string dtype = 0 } +message Datasets + { + repeated dataset datasets = 0 + } message Group { string neurodataTypeDef = 0 @@ -45,6 +49,10 @@ message Group repeated group groups = 0 repeated link links = 0 } +message Groups + { + repeated group groups = 0 + } message Link { string name = 0 @@ -76,7 +84,7 @@ message Schema { string source = 0 string namespace = 0 - string doc = 0 string title = 0 repeated string neurodataTypes = 0 + string doc = 0 } diff --git a/nwb-schema-linkml/project/shacl/nwb_schema_language.shacl.ttl b/nwb-schema-language/project/shacl/nwb_schema_language.shacl.ttl similarity index 100% rename from nwb-schema-linkml/project/shacl/nwb_schema_language.shacl.ttl rename to nwb-schema-language/project/shacl/nwb_schema_language.shacl.ttl diff --git a/nwb-schema-linkml/project/shex/nwb_schema_language.shex b/nwb-schema-language/project/shex/nwb_schema_language.shex similarity index 93% rename from nwb-schema-linkml/project/shex/nwb_schema_language.shex rename to nwb-schema-language/project/shex/nwb_schema_language.shex index 8cf7572..30e934f 100644 --- a/nwb-schema-linkml/project/shex/nwb_schema_language.shex +++ b/nwb-schema-language/project/shex/nwb_schema_language.shex @@ -97,6 +97,12 @@ linkml:Sparqlpath xsd:string ) } + CLOSED { + ( $ @ * ; + rdf:type [ ] ? + ) +} + { ( $ @linkml:String ? ; rdf:type [ ] ? @@ -122,6 +128,12 @@ linkml:Sparqlpath xsd:string ) } + CLOSED { + ( $ @ * ; + rdf:type [ ] ? + ) +} + CLOSED { ( $ ( @linkml:String ? ; @linkml:String ; @@ -169,9 +181,9 @@ linkml:Sparqlpath xsd:string CLOSED { ( $ ( @linkml:String ? ; @linkml:String ? ; - @linkml:String ; @linkml:String ? ; - <neurodata_types> @linkml:String * + <neurodata_types> @linkml:String * ; + <doc> @linkml:String ? ) ; rdf:type [ <Schema> ] ? ) diff --git a/nwb-schema-linkml/project/sqlschema/nwb_schema_language.sql b/nwb-schema-language/project/sqlschema/nwb_schema_language.sql similarity index 90% rename from nwb-schema-linkml/project/sqlschema/nwb_schema_language.sql rename to nwb-schema-language/project/sqlschema/nwb_schema_language.sql index 4dd8369..f890c08 100644 --- a/nwb-schema-linkml/project/sqlschema/nwb_schema_language.sql +++ b/nwb-schema-language/project/sqlschema/nwb_schema_language.sql @@ -36,6 +36,11 @@ CREATE TABLE "Dataset" ( PRIMARY KEY (neurodata_type_def, neurodata_type_inc, name, default_name, dims, shape, value, default_value, doc, quantity, linkable, attributes, dtype) ); +CREATE TABLE "Datasets" ( + datasets TEXT, + PRIMARY KEY (datasets) +); + CREATE TABLE "Group" ( neurodata_type_def TEXT, neurodata_type_inc TEXT, @@ -51,6 +56,11 @@ CREATE TABLE "Group" ( PRIMARY KEY (neurodata_type_def, neurodata_type_inc, name, default_name, doc, quantity, linkable, attributes, datasets, groups, links) ); +CREATE TABLE "Groups" ( + groups TEXT, + PRIMARY KEY (groups) +); + CREATE TABLE "Link" ( name TEXT, doc TEXT NOT NULL, @@ -85,8 +95,8 @@ CREATE TABLE "ReferenceDtype" ( CREATE TABLE "Schema" ( source TEXT, namespace TEXT, - doc TEXT NOT NULL, title TEXT, neurodata_types TEXT, - PRIMARY KEY (source, namespace, doc, title, neurodata_types) + doc TEXT, + PRIMARY KEY (source, namespace, title, neurodata_types, doc) ); diff --git a/nwb-schema-linkml/pyproject.toml b/nwb-schema-language/pyproject.toml similarity index 92% rename from nwb-schema-linkml/pyproject.toml rename to nwb-schema-language/pyproject.toml index da1e480..099c218 100644 --- a/nwb-schema-linkml/pyproject.toml +++ b/nwb-schema-language/pyproject.toml @@ -1,5 +1,5 @@ [tool.poetry] -name = "nwb_schema_linkml" +name = "nwb_schema_language" version = "0.1.0" description = "Translation of the nwb-schema-language to LinkML" authors = ["Jonny Saunders <j@nny.fyi>"] diff --git a/nwb-schema-linkml/src/data/tests/nwb.base.yaml b/nwb-schema-language/src/data/tests/nwb.base.yaml similarity index 100% rename from nwb-schema-linkml/src/data/tests/nwb.base.yaml rename to nwb-schema-language/src/data/tests/nwb.base.yaml diff --git a/nwb-schema-linkml/src/data/tests/nwb.behavior.yaml b/nwb-schema-language/src/data/tests/nwb.behavior.yaml similarity index 100% rename from nwb-schema-linkml/src/data/tests/nwb.behavior.yaml rename to nwb-schema-language/src/data/tests/nwb.behavior.yaml diff --git a/nwb-schema-linkml/src/data/tests/nwb.device.yaml b/nwb-schema-language/src/data/tests/nwb.device.yaml similarity index 100% rename from nwb-schema-linkml/src/data/tests/nwb.device.yaml rename to nwb-schema-language/src/data/tests/nwb.device.yaml diff --git a/nwb-schema-linkml/src/data/tests/nwb.ecephys.yaml b/nwb-schema-language/src/data/tests/nwb.ecephys.yaml similarity index 100% rename from nwb-schema-linkml/src/data/tests/nwb.ecephys.yaml rename to nwb-schema-language/src/data/tests/nwb.ecephys.yaml diff --git a/nwb-schema-linkml/src/data/tests/nwb.epoch.yaml b/nwb-schema-language/src/data/tests/nwb.epoch.yaml similarity index 100% rename from nwb-schema-linkml/src/data/tests/nwb.epoch.yaml rename to nwb-schema-language/src/data/tests/nwb.epoch.yaml diff --git a/nwb-schema-linkml/src/data/tests/nwb.file.yaml b/nwb-schema-language/src/data/tests/nwb.file.yaml similarity index 100% rename from nwb-schema-linkml/src/data/tests/nwb.file.yaml rename to nwb-schema-language/src/data/tests/nwb.file.yaml diff --git a/nwb-schema-linkml/src/data/tests/nwb.icephys.yaml b/nwb-schema-language/src/data/tests/nwb.icephys.yaml similarity index 100% rename from nwb-schema-linkml/src/data/tests/nwb.icephys.yaml rename to nwb-schema-language/src/data/tests/nwb.icephys.yaml diff --git a/nwb-schema-linkml/src/data/tests/nwb.image.yaml b/nwb-schema-language/src/data/tests/nwb.image.yaml similarity index 100% rename from nwb-schema-linkml/src/data/tests/nwb.image.yaml rename to nwb-schema-language/src/data/tests/nwb.image.yaml diff --git a/nwb-schema-linkml/src/data/tests/nwb.misc.yaml b/nwb-schema-language/src/data/tests/nwb.misc.yaml similarity index 100% rename from nwb-schema-linkml/src/data/tests/nwb.misc.yaml rename to nwb-schema-language/src/data/tests/nwb.misc.yaml diff --git a/nwb-schema-linkml/src/data/tests/nwb.namespace.yaml b/nwb-schema-language/src/data/tests/nwb.namespace.yaml similarity index 100% rename from nwb-schema-linkml/src/data/tests/nwb.namespace.yaml rename to nwb-schema-language/src/data/tests/nwb.namespace.yaml diff --git a/nwb-schema-linkml/src/data/tests/nwb.ogen.yaml b/nwb-schema-language/src/data/tests/nwb.ogen.yaml similarity index 100% rename from nwb-schema-linkml/src/data/tests/nwb.ogen.yaml rename to nwb-schema-language/src/data/tests/nwb.ogen.yaml diff --git a/nwb-schema-linkml/src/data/tests/nwb.ophys.yaml b/nwb-schema-language/src/data/tests/nwb.ophys.yaml similarity index 100% rename from nwb-schema-linkml/src/data/tests/nwb.ophys.yaml rename to nwb-schema-language/src/data/tests/nwb.ophys.yaml diff --git a/nwb-schema-linkml/src/data/tests/nwb.retinotopy.yaml b/nwb-schema-language/src/data/tests/nwb.retinotopy.yaml similarity index 100% rename from nwb-schema-linkml/src/data/tests/nwb.retinotopy.yaml rename to nwb-schema-language/src/data/tests/nwb.retinotopy.yaml diff --git a/nwb-schema-linkml/src/docs/about.md b/nwb-schema-language/src/docs/about.md similarity index 100% rename from nwb-schema-linkml/src/docs/about.md rename to nwb-schema-language/src/docs/about.md diff --git a/nwb-schema-language/src/nwb_schema_language/__init__.py b/nwb-schema-language/src/nwb_schema_language/__init__.py new file mode 100644 index 0000000..1db7e97 --- /dev/null +++ b/nwb-schema-language/src/nwb_schema_language/__init__.py @@ -0,0 +1,9 @@ +from .datamodel.nwb_schema_pydantic import Namespace, \ + Namespaces, \ + Schema, \ + Group, \ + Attribute, \ + Link, \ + Dataset, \ + ReferenceDtype, \ + CompoundDtype diff --git a/nwb-schema-linkml/src/nwb_schema_language/_version.py b/nwb-schema-language/src/nwb_schema_language/_version.py similarity index 100% rename from nwb-schema-linkml/src/nwb_schema_language/_version.py rename to nwb-schema-language/src/nwb_schema_language/_version.py diff --git a/nwb-schema-linkml/src/nwb_schema_language/datamodel/__init__.py b/nwb-schema-language/src/nwb_schema_language/datamodel/__init__.py similarity index 100% rename from nwb-schema-linkml/src/nwb_schema_language/datamodel/__init__.py rename to nwb-schema-language/src/nwb_schema_language/datamodel/__init__.py diff --git a/nwb-schema-linkml/src/nwb_schema_language/datamodel/nwb_schema_language.py b/nwb-schema-language/src/nwb_schema_language/datamodel/nwb_schema_language.py similarity index 91% rename from nwb-schema-linkml/src/nwb_schema_language/datamodel/nwb_schema_language.py rename to nwb-schema-language/src/nwb_schema_language/datamodel/nwb_schema_language.py index 852408f..f010dc6 100644 --- a/nwb-schema-linkml/src/nwb_schema_language/datamodel/nwb_schema_language.py +++ b/nwb-schema-language/src/nwb_schema_language/datamodel/nwb_schema_language.py @@ -1,5 +1,5 @@ # Auto generated from nwb_schema_language.yaml by pythongen.py version: 0.0.1 -# Generation date: 2023-08-16T23:21:37 +# Generation date: 2023-08-18T00:36:55 # Schema: nwb-schema-language # # id: https://w3id.org/p2p_ld/nwb-schema-language @@ -95,7 +95,6 @@ class Namespace(YAMLRoot): if self.date is not None and not isinstance(self.date, XSDDate): self.date = XSDDate(self.date) - print(self.schema) if not isinstance(self.schema, list): self.schema = [self.schema] if self.schema is not None else [] self.schema = [v if isinstance(v, Schema) else Schema(**as_dict(v)) for v in self.schema] @@ -115,7 +114,9 @@ class Namespaces(YAMLRoot): namespaces: Optional[Union[Union[dict, Namespace], List[Union[dict, Namespace]]]] = empty_list() def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - self._normalize_inlined_as_dict(slot_name="namespaces", slot_type=Namespace, key_name="doc", keyed=False) + if not isinstance(self.namespaces, list): + self.namespaces = [self.namespaces] if self.namespaces is not None else [] + self.namespaces = [v if isinstance(v, Namespace) else Namespace(**as_dict(v)) for v in self.namespaces] super().__post_init__(**kwargs) @@ -129,18 +130,13 @@ class Schema(YAMLRoot): class_name: ClassVar[str] = "Schema" class_model_uri: ClassVar[URIRef] = NWB_SCHEMA_LANGUAGE.Schema - doc: str = None source: Optional[str] = None namespace: Optional[str] = None title: Optional[str] = None neurodata_types: Optional[Union[str, List[str]]] = empty_list() + doc: Optional[str] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.doc): - self.MissingRequiredField("doc") - if not isinstance(self.doc, str): - self.doc = str(self.doc) - if self.source is not None and not isinstance(self.source, str): self.source = str(self.source) @@ -154,6 +150,9 @@ class Schema(YAMLRoot): self.neurodata_types = [self.neurodata_types] if self.neurodata_types is not None else [] self.neurodata_types = [v if isinstance(v, str) else str(v) for v in self.neurodata_types] + if self.doc is not None and not isinstance(self.doc, str): + self.doc = str(self.doc) + super().__post_init__(**kwargs) @@ -204,15 +203,38 @@ class Group(YAMLRoot): self._normalize_inlined_as_dict(slot_name="attributes", slot_type=Attribute, key_name="name", keyed=False) - self._normalize_inlined_as_dict(slot_name="datasets", slot_type=Dataset, key_name="doc", keyed=False) + if not isinstance(self.datasets, list): + self.datasets = [self.datasets] if self.datasets is not None else [] + self.datasets = [v if isinstance(v, Dataset) else Dataset(**as_dict(v)) for v in self.datasets] - self._normalize_inlined_as_dict(slot_name="groups", slot_type=Group, key_name="doc", keyed=False) + if not isinstance(self.groups, list): + self.groups = [self.groups] if self.groups is not None else [] + self.groups = [v if isinstance(v, Group) else Group(**as_dict(v)) for v in self.groups] self._normalize_inlined_as_dict(slot_name="links", slot_type=Link, key_name="doc", keyed=False) super().__post_init__(**kwargs) +@dataclass +class Groups(YAMLRoot): + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = NWB_SCHEMA_LANGUAGE.Groups + class_class_curie: ClassVar[str] = "nwb_schema_language:Groups" + class_name: ClassVar[str] = "Groups" + class_model_uri: ClassVar[URIRef] = NWB_SCHEMA_LANGUAGE.Groups + + groups: Optional[Union[Union[dict, Group], List[Union[dict, Group]]]] = empty_list() + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if not isinstance(self.groups, list): + self.groups = [self.groups] if self.groups is not None else [] + self.groups = [v if isinstance(v, Group) else Group(**as_dict(v)) for v in self.groups] + + super().__post_init__(**kwargs) + + @dataclass class Attribute(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -356,6 +378,25 @@ class Dataset(YAMLRoot): super().__post_init__(**kwargs) +@dataclass +class Datasets(YAMLRoot): + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = NWB_SCHEMA_LANGUAGE.Datasets + class_class_curie: ClassVar[str] = "nwb_schema_language:Datasets" + class_name: ClassVar[str] = "Datasets" + class_model_uri: ClassVar[URIRef] = NWB_SCHEMA_LANGUAGE.Datasets + + datasets: Optional[Union[Union[dict, Dataset], List[Union[dict, Dataset]]]] = empty_list() + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if not isinstance(self.datasets, list): + self.datasets = [self.datasets] if self.datasets is not None else [] + self.datasets = [v if isinstance(v, Dataset) else Dataset(**as_dict(v)) for v in self.datasets] + + super().__post_init__(**kwargs) + + @dataclass class ReferenceDtype(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -674,12 +715,12 @@ slots.target_type = Slot(uri=NWB_SCHEMA_LANGUAGE.target_type, name="target_type" slots.reftype = Slot(uri=NWB_SCHEMA_LANGUAGE.reftype, name="reftype", curie=NWB_SCHEMA_LANGUAGE.curie('reftype'), model_uri=NWB_SCHEMA_LANGUAGE.reftype, domain=None, range=Optional[Union[str, "ReftypeOptions"]]) +slots.schema__doc = Slot(uri=NWB_SCHEMA_LANGUAGE.doc, name="schema__doc", curie=NWB_SCHEMA_LANGUAGE.curie('doc'), + model_uri=NWB_SCHEMA_LANGUAGE.schema__doc, domain=None, range=Optional[str]) + slots.Namespace_name = Slot(uri=NWB_SCHEMA_LANGUAGE.name, name="Namespace_name", curie=NWB_SCHEMA_LANGUAGE.curie('name'), model_uri=NWB_SCHEMA_LANGUAGE.Namespace_name, domain=Namespace, range=str) -slots.Schema_doc = Slot(uri=NWB_SCHEMA_LANGUAGE.doc, name="Schema_doc", curie=NWB_SCHEMA_LANGUAGE.curie('doc'), - model_uri=NWB_SCHEMA_LANGUAGE.Schema_doc, domain=Schema, range=str) - slots.Attribute_name = Slot(uri=NWB_SCHEMA_LANGUAGE.name, name="Attribute_name", curie=NWB_SCHEMA_LANGUAGE.curie('name'), model_uri=NWB_SCHEMA_LANGUAGE.Attribute_name, domain=Attribute, range=str) diff --git a/nwb-schema-language/src/nwb_schema_language/datamodel/nwb_schema_pydantic.py b/nwb-schema-language/src/nwb_schema_language/datamodel/nwb_schema_pydantic.py new file mode 100644 index 0000000..95f8bd6 --- /dev/null +++ b/nwb-schema-language/src/nwb_schema_language/datamodel/nwb_schema_pydantic.py @@ -0,0 +1,241 @@ +from __future__ import annotations +from datetime import datetime, date +from enum import Enum +from typing import List, Dict, Optional, Any, Union +from pydantic import BaseModel as BaseModel, Field +import sys +if sys.version_info >= (3, 8): + from typing import Literal +else: + from typing_extensions import Literal + + +metamodel_version = "None" +version = "None" + +class WeakRefShimBaseModel(BaseModel): + __slots__ = '__weakref__' + +class ConfiguredBaseModel(WeakRefShimBaseModel, + validate_assignment = True, + validate_all = True, + underscore_attrs_are_private = True, + extra = 'forbid', + arbitrary_types_allowed = True, + use_enum_values = True): + pass + + +class ReftypeOptions(str, Enum): + + # Reference to another group or dataset of the given target_type + ref = "ref" + # Reference to another group or dataset of the given target_type + reference = "reference" + # Reference to another group or dataset of the given target_type + object = "object" + # Reference to a region (i.e. subset) of another dataset of the given target_type + region = "region" + + + +class QuantityEnum(str, Enum): + + # Zero or more instances, equivalent to zero_or_many + ASTERISK = "*" + # Zero or one instances, equivalent to zero_or_one + QUESTION_MARK = "?" + # One or more instances, equivalent to one_or_many + PLUS_SIGN = "+" + # Zero or more instances, equivalent to * + zero_or_many = "zero_or_many" + # One or more instances, equivalent to + + one_or_many = "one_or_many" + # Zero or one instances, equivalent to ? + zero_or_one = "zero_or_one" + + + +class FlatDtype(str, Enum): + + # single precision floating point (32 bit) + float = "float" + # single precision floating point (32 bit) + float32 = "float32" + # double precision floating point (64 bit) + double = "double" + # double precision floating point (64 bit) + float64 = "float64" + # signed 64 bit integer + long = "long" + # signed 64 bit integer + int64 = "int64" + # signed 32 bit integer + int = "int" + # signed 32 bit integer + int32 = "int32" + # signed 16 bit integer + int16 = "int16" + # signed 16 bit integer + short = "short" + # signed 8 bit integer + int8 = "int8" + # unsigned 32 bit integer + uint = "uint" + # unsigned 32 bit integer + uint32 = "uint32" + # unsigned 16 bit integer + uint16 = "uint16" + # unsigned 8 bit integer + uint8 = "uint8" + # unsigned 64 bit integer + uint64 = "uint64" + # any numeric type (i.e., any int, uint, float) + numeric = "numeric" + # 8-bit Unicode + text = "text" + # 8-bit Unicode + utf = "utf" + # 8-bit Unicode + utf8 = "utf8" + # 8-bit Unicode + utf_8 = "utf-8" + # ASCII text + ascii = "ascii" + # 8 bit integer with valid values 0 or 1 + bool = "bool" + # ISO 8601 datetime string + isodatetime = "isodatetime" + + + +class Namespace(ConfiguredBaseModel): + + doc: str = Field(..., description="""Description of corresponding object.""") + name: str = Field(...) + full_name: Optional[str] = Field(None, description="""Optional string with extended full name for the namespace.""") + version: str = Field(...) + date: Optional[date] = Field(None, description="""Date that a namespace was last modified or released""") + author: List[str] = Field(default_factory=list, description="""List of strings with the names of the authors of the namespace.""") + contact: List[str] = Field(default_factory=list, description="""List of strings with the contact information for the authors. Ordering of the contacts should match the ordering of the authors.""") + schema_: Optional[List[Schema]] = Field(alias="schema", default_factory=list, description="""List of the schema to be included in this namespace.""") + + +class Namespaces(ConfiguredBaseModel): + + namespaces: Optional[List[Namespace]] = Field(default_factory=list) + + +class Schema(ConfiguredBaseModel): + + source: Optional[str] = Field(None, description="""describes the name of the YAML (or JSON) file with the schema specification. The schema files should be located in the same folder as the namespace file.""") + namespace: Optional[str] = Field(None, description="""describes a named reference to another namespace. In contrast to source, this is a reference by name to a known namespace (i.e., the namespace is resolved during the build and must point to an already existing namespace). This mechanism is used to allow, e.g., extension of a core namespace (here the NWB core namespace) without requiring hard paths to the files describing the core namespace. Either source or namespace must be specified, but not both.""") + title: Optional[str] = Field(None, description="""a descriptive title for a file for documentation purposes.""") + neurodata_types: Optional[List[Union[Dataset, Group]]] = Field(default_factory=list, description="""an optional list of strings indicating which data types should be included from the given specification source or namespace. The default is null indicating that all data types should be included.""") + doc: Optional[str] = Field(None) + + +class Groups(ConfiguredBaseModel): + + groups: Optional[List[Group]] = Field(default_factory=list) + + +class Link(ConfiguredBaseModel): + + name: Optional[str] = Field(None) + doc: str = Field(..., description="""Description of corresponding object.""") + target_type: str = Field(..., description="""Describes the neurodata_type of the target that the reference points to""") + quantity: Optional[Union[QuantityEnum, int]] = Field(1) + + +class Datasets(ConfiguredBaseModel): + + datasets: Optional[List[Dataset]] = Field(default_factory=list) + + +class ReferenceDtype(ConfiguredBaseModel): + + target_type: str = Field(..., description="""Describes the neurodata_type of the target that the reference points to""") + reftype: Optional[ReftypeOptions] = Field(None, description="""describes the kind of reference""") + + +class CompoundDtype(ConfiguredBaseModel): + + name: str = Field(...) + doc: str = Field(..., description="""Description of corresponding object.""") + dtype: Union[FlatDtype, ReferenceDtype] = Field(...) + + +class DtypeMixin(ConfiguredBaseModel): + + dtype: Optional[List[Union[CompoundDtype, FlatDtype, ReferenceDtype]]] = Field(default_factory=list) + + +class Attribute(DtypeMixin): + + name: str = Field(...) + dims: Optional[List[str]] = Field(default_factory=list) + shape: Optional[List[str]] = Field(default_factory=list) + value: Optional[Any] = Field(None, description="""Optional constant, fixed value for the attribute.""") + default_value: Optional[Any] = Field(None, description="""Optional default value for variable-valued attributes.""") + doc: str = Field(..., description="""Description of corresponding object.""") + required: Optional[bool] = Field(True, description="""Optional boolean key describing whether the attribute is required. Default value is True.""") + dtype: Optional[List[Union[CompoundDtype, FlatDtype, ReferenceDtype]]] = Field(default_factory=list) + + +class NamingMixin(ConfiguredBaseModel): + """ + require either neurodata_type_def or name to be present + """ + None + + +class Group(NamingMixin): + + neurodata_type_def: Optional[str] = Field(None) + neurodata_type_inc: Optional[str] = Field(None) + name: Optional[str] = Field(None) + default_name: Optional[str] = Field(None) + doc: str = Field(..., description="""Description of corresponding object.""") + quantity: Optional[Union[QuantityEnum, int]] = Field(1) + linkable: Optional[bool] = Field(None) + attributes: Optional[List[Attribute]] = Field(default_factory=list) + datasets: Optional[List[Dataset]] = Field(default_factory=list) + groups: Optional[List[Group]] = Field(default_factory=list) + links: Optional[List[Link]] = Field(default_factory=list) + + +class Dataset(NamingMixin, DtypeMixin): + + neurodata_type_def: Optional[str] = Field(None) + neurodata_type_inc: Optional[str] = Field(None) + name: Optional[str] = Field(None) + default_name: Optional[str] = Field(None) + dims: Optional[List[str]] = Field(default_factory=list) + shape: Optional[List[str]] = Field(default_factory=list) + value: Optional[Any] = Field(None, description="""Optional constant, fixed value for the attribute.""") + default_value: Optional[Any] = Field(None, description="""Optional default value for variable-valued attributes.""") + doc: str = Field(..., description="""Description of corresponding object.""") + quantity: Optional[Union[QuantityEnum, int]] = Field(1) + linkable: Optional[bool] = Field(None) + attributes: Optional[List[Attribute]] = Field(default_factory=list) + dtype: Optional[List[Union[CompoundDtype, FlatDtype, ReferenceDtype]]] = Field(default_factory=list) + + + +# Update forward refs +# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ +Namespace.update_forward_refs() +Namespaces.update_forward_refs() +Schema.update_forward_refs() +Groups.update_forward_refs() +Link.update_forward_refs() +Datasets.update_forward_refs() +ReferenceDtype.update_forward_refs() +CompoundDtype.update_forward_refs() +DtypeMixin.update_forward_refs() +Attribute.update_forward_refs() +NamingMixin.update_forward_refs() +Group.update_forward_refs() +Dataset.update_forward_refs() + diff --git a/nwb-schema-linkml/src/nwb_schema_language/schema/nwb_schema_language.yaml b/nwb-schema-language/src/nwb_schema_language/schema/nwb_schema_language.yaml similarity index 96% rename from nwb-schema-linkml/src/nwb_schema_language/schema/nwb_schema_language.yaml rename to nwb-schema-language/src/nwb_schema_language/schema/nwb_schema_language.yaml index 98cabc7..7b33d57 100644 --- a/nwb-schema-linkml/src/nwb_schema_language/schema/nwb_schema_language.yaml +++ b/nwb-schema-language/src/nwb_schema_language/schema/nwb_schema_language.yaml @@ -46,10 +46,9 @@ classes: slots: - source - namespace - - doc - title - neurodata_types - slot_usage: + attributes: doc: required: false rules: @@ -82,6 +81,10 @@ classes: - groups - links + Groups: + slots: + - groups + Attribute: mixins: - DtypeMixin @@ -122,6 +125,10 @@ classes: - linkable - attributes + Datasets: + slots: + - datasets + ReferenceDtype: slots: - target_type @@ -137,7 +144,10 @@ classes: required: true dtype: required: true - range: FlatDtype + any_of: + - range: ReferenceDtype + - range: FlatDtype + multivalued: false DtypeMixin: mixin: true @@ -216,6 +226,7 @@ slots: namespaces: multivalued: true range: Namespace + inlined_as_list: true neurodata_types: multivalued: true any_of: @@ -256,19 +267,22 @@ slots: datasets: range: Dataset multivalued: true + inlined_as_list: true groups: range: Group multivalued: true + inlined_as_list: true links: range: Link multivalued: true # attributes dtype: - exactly_one_of: + any_of: - range: FlatDtype - range: CompoundDtype - range: ReferenceDtype + multivalued: true dims: multivalued: true range: string @@ -298,9 +312,9 @@ slots: description: Describes the neurodata_type of the target that the reference points to required: true - any_of: - - range: Dataset - - range: Group +# any_of: +# - range: Dataset +# - range: Group reftype: description: describes the kind of reference range: reftype_options diff --git a/nwb-schema-linkml/tests/__init__.py b/nwb-schema-language/tests/__init__.py similarity index 100% rename from nwb-schema-linkml/tests/__init__.py rename to nwb-schema-language/tests/__init__.py diff --git a/nwb-schema-linkml/tests/test_data.py b/nwb-schema-language/tests/test_data.py similarity index 100% rename from nwb-schema-linkml/tests/test_data.py rename to nwb-schema-language/tests/test_data.py diff --git a/nwb-schema-linkml/utils/get-value.sh b/nwb-schema-language/utils/get-value.sh similarity index 100% rename from nwb-schema-linkml/utils/get-value.sh rename to nwb-schema-language/utils/get-value.sh diff --git a/nwb-schema-linkml/project/excel/nwb_schema_language.xlsx b/nwb-schema-linkml/project/excel/nwb_schema_language.xlsx deleted file mode 100644 index e8a38c6..0000000 Binary files a/nwb-schema-linkml/project/excel/nwb_schema_language.xlsx and /dev/null differ diff --git a/nwb-schema-linkml/src/nwb_schema_language/__init__.py b/nwb_linkml/__init__.py similarity index 100% rename from nwb-schema-linkml/src/nwb_schema_language/__init__.py rename to nwb_linkml/__init__.py diff --git a/translate_nwb/constants.py b/nwb_linkml/constants.py similarity index 100% rename from translate_nwb/constants.py rename to nwb_linkml/constants.py diff --git a/nwb_linkml/io.py b/nwb_linkml/io.py new file mode 100644 index 0000000..5e54283 --- /dev/null +++ b/nwb_linkml/io.py @@ -0,0 +1,49 @@ +""" +Loading/saving NWB Schema yaml files +""" +from pathlib import Path +from typing import TypedDict, List +from pprint import pprint + +from linkml_runtime.loaders import yaml_loader +import yaml + +from nwb_schema_language import Namespaces, Group, Dataset +from nwb_linkml.namespaces import GitRepo, NamespaceRepo + + + +def load_namespaces(path:Path|NamespaceRepo) -> Namespaces: + if isinstance(path, NamespaceRepo): + path = path.provide_from_git() + + namespaces = yaml_loader.load(str(path), target_class=Namespaces) + return namespaces + +class SchemaFile(TypedDict): + datasets: List[Dataset] + groups: List[Group] + +def load_schema_file(path:Path) -> List[Dataset | Group]: + with open(path, 'r') as yfile: + source = yaml.safe_load(yfile) + + schema = [] + + for dataset in source.get('datasets', []): + try: + schema.append(Dataset(**dataset)) + except Exception as e: + pprint(dataset) + raise e + + #schema.extend([Dataset(**dataset) for dataset in source.get('datasets', [])]) + #schema.extend([Group(**group) for group in source.get('groups', [])]) + return schema + + + + + + + diff --git a/translate_nwb/__init__.py b/nwb_linkml/maps/__init__.py similarity index 100% rename from translate_nwb/__init__.py rename to nwb_linkml/maps/__init__.py diff --git a/nwb_linkml/namespaces.py b/nwb_linkml/namespaces.py new file mode 100644 index 0000000..f6578c8 --- /dev/null +++ b/nwb_linkml/namespaces.py @@ -0,0 +1,172 @@ +""" +Define and manage NWB namespaces in external repositories +""" +import warnings +from pathlib import Path +import tempfile +import subprocess +import shutil + +from pydantic import BaseModel, HttpUrl, FilePath, DirectoryPath, Field + +class NamespaceRepo(BaseModel): + """ + Definition of one NWB namespaces file to import from a git repository + """ + name: str = Field(description="Short name used to refer to this namespace (usually equivalent to the name field within a namespaces NWB list)") + repository: HttpUrl | DirectoryPath = Field(description="URL or local absolute path to the root repository") + path: Path = Field(description="Relative path from the repository root to the namespace file") + + def provide_from_git(self, commit:str|None=None) -> Path: + git = GitRepo(self, commit) + git.clone() + return git.namespace_file + +# Constant namespaces +NWB_CORE_REPO = NamespaceRepo( + name="core", + repository="https://github.com/NeurodataWithoutBorders/nwb-schema", + path=Path("core/nwb.namespace.yaml") +) + +HDMF_COMMON_REPO = NamespaceRepo( + name="hdmf-common", + repository="https://github.com/hdmf-dev/hdmf-common-schema", + path=Path("common/namespace.yaml") +) + +DEFAULT_REPOS = { + repo.name: repo for repo in [NWB_CORE_REPO, HDMF_COMMON_REPO] +} + + +class GitError(OSError): + pass + +class GitRepo: + """ + Manage a temporary git repository that provides the NWB yaml files + """ + def __init__(self, namespace:NamespaceRepo, commit:str|None=None): + self._temp_directory = None + self.namespace = namespace + self.commit = commit + + def _git_call(self, *args) -> subprocess.CompletedProcess: + res = subprocess.run( + ['git', '-C', self.temp_directory, *args], + capture_output=True + ) + if res.returncode != 0: + raise GitError(f'Git call did not complete successfully.\n---\nCall: {args}\nResult: {res.stderr}') + return res + + @property + def temp_directory(self) -> Path: + """ + Temporary directory where this repository will be cloned to + """ + if self._temp_directory is None: + self._temp_directory = Path(tempfile.gettempdir()) / f'nwb_linkml__{self.namespace.name}' + if self._temp_directory.exists(): + warnings.warn(f'Temporary directory already exists! {self._temp_directory}') + else: + self._temp_directory.mkdir(parents=True) + + return self._temp_directory + + @property + def remote(self) -> str: + """ + URL for "origin" remote + """ + res = self._git_call('remote', 'get-url', 'origin') + return res.stdout.decode('utf-8').strip() + + @property + def active_commit(self) -> str: + """ + Currently checked out commit + """ + res = self._git_call('rev-parse', 'HEAD') + commit = res.stdout.decode('utf-8').strip() + return commit + + @property + def namespace_file(self) -> Path: + """ + Local path to the indicated namespace file. + """ + return self.temp_directory / self.namespace.path + + def check(self) -> bool: + """ + Check if the repository is already cloned and checked out + + Returns: + (bool) True if present, False if not + """ + if not any(self.temp_directory.iterdir()): + # directory is empty + return False + + try: + # check our commit, this also checks if we're a git repo + if self.active_commit != self.commit and self.commit is not None: + warnings.warn('At wrong commit') + return False + + except GitError: + return False + + # Check that the remote matches + if self.remote.strip('.git') != self.namespace.repository: + warnings.warn('Repository exists, but has the wrong remote URL') + return False + + # otherwise we're good + return True + + def cleanup(self): + """ + Delete contents of temporary directory + """ + if not str(self.temp_directory).startswith(tempfile.gettempdir()): + warnings.warn('Temp directory is outside of the system temp dir, not deleting in case this has been changed by mistake') + self._temp_directory = None + return + + shutil.rmtree(str(self.temp_directory)) + self._temp_directory = None + + def clone(self, force:bool=False): + """ + Clone the repository into the temporary directory + + Args: + force (bool): If files are present in the temp directory, delete them + + Raises: + :class:`.GitError` - if the repository can't be cloned + """ + if any(self.temp_directory.iterdir()): + if force: + self.cleanup() + else: + if not self.check(): + warnings.warn('Destination directory is not empty and does not pass checks for correctness! pass force to overwrite') + return + + res = subprocess.run(['git', 'clone', str(self.namespace.repository), str(self.temp_directory)]) + if res.returncode != 0: + raise GitError(f'Could not clone repository:\n{res.stderr}') + + + + + + + + + + diff --git a/poetry.lock b/poetry.lock index b9ab16e..fb19e82 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,212 +1,9 @@ -# This file is automatically @generated by Poetry and should not be 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