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Publish draft #308

Merged
merged 6 commits into from
Apr 11, 2024
Merged

Publish draft #308

merged 6 commits into from
Apr 11, 2024

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HadleyKing
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HadleyKing and others added 6 commits April 4, 2024 20:26
@HadleyKing
Add DraftsModifyApi
c7f4827 
Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/selectors.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	modified:   prefix/selectors.py
	deleted:    tests/test_apis/test_biocompute/objects_drafts_create.py
	deleted:    tests/test_apis/test_biocompute/test_objects_drafts_create.py
@HadleyKing
Add IEEE schema
9d8737d 
Changes to be committed:
	new file:   .secrets
	new file:   config/IEEE/2791object.json
	new file:   config/IEEE/description_domain.json
	new file:   config/IEEE/error_domain.json
	new file:   config/IEEE/execution_domain.json
	new file:   config/IEEE/io_domain.json
	new file:   config/IEEE/parametric_domain.json
	new file:   config/IEEE/provenance_domain.json
	new file:   config/IEEE/usability_domain.json
@HadleyKing
test_objects_drafts_create
98da7ca 
Changes to be committed:
	new file:   tests/test_apis/test_biocompute/test_objects_drafts_create.py
@HadleyKing
Fix test
c0dafbd 
Changes to be committed:
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_create.py
@HadleyKing
Enable publish bco endpoint
9246ed6 
This included a great many supporting functions
and permission checks to accomplish. Also added
the validate functions to the codebase

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/selectors.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	modified:   config/services.py
	modified:   docs/refactor.md
	modified:   prefix/selectors.py
	new file:   tests/test_apis/test_biocompute/test_objects_drafts_publish.py
@HadleyKing
Merge branch 'model_refactor' into publish_draft
b6971a6
@HadleyKing HadleyKing merged commit 8ee1039 into model_refactor Apr 11, 2024
2 checks passed
@HadleyKing HadleyKing deleted the publish_draft branch April 11, 2024 16:07
HadleyKing added a commit that referenced this pull request May 20, 2024
@HadleyKing @tianywan819 @acoleman2000
Model refactor (#280)
2c4e0d2 
* Change `bcodb` directory to `config` directory

Changes to be committed:
	modified:   .gitignore
	deleted:    bcodb/settings.py
	renamed:    bcodb/__init__.py -> config/__init__.py
	renamed:    bcodb/asgi.py -> config/asgi.py
	renamed:    bcodb/fixtures/local_data.json -> config/fixtures/local_data.json
	renamed:    bcodb/fixtures/test_portal.json -> config/fixtures/test_portal.json
	renamed:    bcodb/urls.py -> config/urls.py
	renamed:    bcodb/wsgi.py -> config/wsgi.py
	modified:   manage.py

* Create NewUser model and remove new_user model

changed model behind `/api/accounts/new/`
Changes to be committed:
	modified:   api/admin.py
	new file:   api/migrations/0006_delete_new_users.py
	modified:   api/models.py
	deleted:    api/scripts/method_specific/POST_api_accounts_new.py
	modified:   api/urls.py
	modified:   api/views.py
	modified:   authentication/admin.py
	modified:   authentication/apis.py
	new file:   authentication/migrations/0002_newuser.py
	modified:   authentication/models.py
	modified:   authentication/selectors.py
	modified:   authentication/services.py
	modified:   tests/fixtures/test_data.json
	modified:   tests/test_views/test_api_account_activate.py
	modified:   tests/test_views/test_api_account_new.py

* Add example values to test account request

Changes to be committed:
	modified:   authentication/apis.py
	new file:   docs/refactor.md

* Account activation has been enabled.

On branch account_authorization
Changes to be committed:
	modified:   api/urls.py
	modified:   api/views.py
	modified:   authentication/apis.py
	modified:   authentication/selectors.py
	modified:   authentication/services.py
	modified:   authentication/urls.py

* Account authorization (#277)

* Account activation has been enabled.

On branch account_authorization
Changes to be committed:
	modified:   api/urls.py
	modified:   api/views.py
	modified:   authentication/apis.py
	modified:   authentication/selectors.py
	modified:   authentication/services.py
	modified:   authentication/urls.py

* get_new_user

* Remove API app
Changes to be committed:
	deleted:    api/__init__.py
	deleted:    api/admin.py
	deleted:    api/apps.py
	deleted:    api/fixtures/bootstrap.json
	deleted:    api/fixtures/metafixtures
	deleted:    api/fixtures/metafixtures.json
	deleted:    api/keys.sh
	deleted:    api/migrations/0001_initial.py
	deleted:    api/migrations/0002_auto_20220124_2356.py
	deleted:    api/migrations/0003_rename_meta_table_prefix_table.py
	deleted:    api/migrations/0004_rename_group_info_groupinfo.py
	deleted:    api/migrations/0005_rename_prefixes_prefix.py
	deleted:    api/migrations/0006_delete_new_users.py
	deleted:    api/migrations/__init__.py
	deleted:    api/model/__init__.py
	deleted:    api/model/groups.py
	deleted:    api/model/prefix.py
	deleted:    api/models.py
	deleted:    api/permissions.py
	deleted:    api/rdb.sh
	deleted:    api/request_definitions/GET.schema
	deleted:    api/request_definitions/POST.schema
	deleted:    api/request_definitions/templates/DELETE_delete_object_by_id.schema
	deleted:    api/request_definitions/templates/GET_activate_account.schema
	deleted:    api/request_definitions/templates/GET_get_object_by_id.schema
	deleted:    api/request_definitions/templates/GET_retrieve_available_schema.schema
	deleted:    api/request_definitions/templates/POST_convert_existing_object_between_schemas.schema
	deleted:    api/request_definitions/templates/POST_convert_payload_to_schema.schema
	deleted:    api/request_definitions/templates/POST_new_account.schema
	deleted:    api/request_definitions/templates/POST_object_listing_by_token.schema
	deleted:    api/request_definitions/templates/POST_objects_draft.schema
	deleted:    api/request_definitions/templates/POST_objects_publish.schema
	deleted:    api/request_definitions/templates/POST_read_object.schema
	deleted:    api/request_definitions/templates/POST_validate_payload_against_schema.schema
	deleted:    api/scripts/__init__.py
	deleted:    api/scripts/method_specific/GET_draft_object_by_id.py
	deleted:    api/scripts/method_specific/GET_published_object_by_id.py
	deleted:    api/scripts/method_specific/GET_published_object_by_id_with_version.py
	deleted:    api/scripts/method_specific/GET_retrieve_available_schema.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_create.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_delete.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_modify.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_permissions.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_permissions_set.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_publish.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_read.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_token.py
	deleted:    api/scripts/method_specific/POST_api_objects_publish.py
	deleted:    api/scripts/method_specific/POST_api_objects_published.py
	deleted:    api/scripts/method_specific/POST_api_objects_search.py
	deleted:    api/scripts/method_specific/POST_api_objects_token.py
	deleted:    api/scripts/method_specific/POST_validate_payload_against_schema.py
	deleted:    api/scripts/method_specific/__init__.py
	deleted:    api/scripts/utilities/DbUtils.py
	deleted:    api/scripts/utilities/FileUtils.py
	deleted:    api/scripts/utilities/JsonUtils.py
	deleted:    api/scripts/utilities/RequestUtils.py
	deleted:    api/scripts/utilities/ResponseUtils.py
	deleted:    api/scripts/utilities/SettingsUtils.py
	deleted:    api/scripts/utilities/UserUtils.py
	deleted:    api/scripts/utilities/__init__.py
	deleted:    api/serializers.py
	deleted:    api/signals.py
	deleted:    api/templates/api/account_activation_message.html
	deleted:    api/urls.py
	deleted:    api/validation_definitions/IEEE/2791object.json
	deleted:    api/validation_definitions/IEEE/description_domain.json
	deleted:    api/validation_definitions/IEEE/error_domain.json
	deleted:    api/validation_definitions/IEEE/execution_domain.json
	deleted:    api/validation_definitions/IEEE/io_domain.json
	deleted:    api/validation_definitions/IEEE/parametric_domain.json
	deleted:    api/validation_definitions/IEEE/provenance_domain.json
	deleted:    api/validation_definitions/IEEE/usability_domain.json
	deleted:    api/validation_definitions/IEEE_sub/IEEE2791-2020.schema
	deleted:    api/validation_definitions/IEEE_sub/domains/description_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/error_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/execution_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/io_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/parametric_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/provenance_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/usability_domain.json
	deleted:    api/validation_definitions/uri_external
	deleted:    api/views.py
	new file:   config/settings.py
	modified:   config/urls.py

Changes not staged for commit:
	modified:   authentication/apis.py
	modified:   authentication/migrations/0001_initial.py
	deleted:    authentication/migrations/0002_newuser.py
	modified:   authentication/services.py
	modified:   docs/refactor.md
	modified:   search/selectors.py
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_database.py
	deleted:    tests/test_fixtures.py
	deleted:    tests/test_models
	modified:   tests/test_views/test_api_account_activate.py
	deleted:    tests/test_views/test_api_accounts_describe.py
	modified:   tests/test_views/test_api_auth_add.py
	modified:   tests/test_views/test_api_auth_reset_token.py
	deleted:    tests/test_views/test_api_groups_group_info.py
	deleted:    tests/test_views/test_api_groups_modify.py
	deleted:    tests/test_views/test_api_objects.py
	deleted:    tests/test_views/test_api_objects_drafts_create.py
	deleted:    tests/test_views/test_api_objects_drafts_modify.py
	deleted:    tests/test_views/test_api_objects_drafts_publish.py
	deleted:    tests/test_views/test_api_objects_search.py
	deleted:    tests/test_views/test_api_objects_validate.py
	deleted:    tests/test_views/test_api_prefixes_create.py
	deleted:    tests/test_views/test_api_prefixes_token.py
	deleted:    tests/test_views/test_get_object_id_draft.py
	deleted:    tests/test_views/test_get_objectid.py
	deleted:    tests/test_views/test_published_object_by_id.py
	modified:   token.json

* Framework for BioCompute model

Changes to be committed:
	new file:   biocompute/__init__.py
	new file:   biocompute/admin.py
	new file:   biocompute/apis.py
	new file:   biocompute/migrations/__init__.py
	new file:   biocompute/models.py
	new file:   biocompute/selectors.py
	new file:   biocompute/services.py
	new file:   biocompute/urls.py

* Added files for Prefix model

Changes to be committed:
	new file:   prefix/__init__.py
	new file:   prefix/admin.py
	new file:   prefix/apis.py
	new file:   prefix/apps.py
	new file:   prefix/migrations/__init__.py
	new file:   prefix/models.py
	new file:   prefix/selectors.py
	new file:   prefix/services.py
	new file:   prefix/urls.py

* Tests for authentication

Changes to be committed:
	modified:   .gitignore
	modified:   authentication/apis.py
	modified:   authentication/migrations/0001_initial.py
	deleted:    authentication/migrations/0002_newuser.py
	modified:   authentication/services.py
	new file:   biocompute/migrations/0001_initial.py
	modified:   docs/refactor.md
	new file:   prefix/migrations/0001_initial.py
	modified:   search/selectors.py
	new file:   test.json
	new file:   tests/fixtures/old_test_data.json
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_database.py
	deleted:    tests/test_fixtures.py
	deleted:    tests/test_models
	modified:   tests/test_views/test_api_account_activate.py
	renamed:    tests/test_views/test_api_accounts_describe.py -> tests/test_views/test_api_account_describe.py
	modified:   tests/test_views/test_api_auth_add.py
	modified:   tests/test_views/test_api_auth_reset_token.py
	deleted:    tests/test_views/test_api_groups_group_info.py
	deleted:    tests/test_views/test_api_groups_modify.py
	deleted:    tests/test_views/test_api_objects.py
	deleted:    tests/test_views/test_api_objects_drafts_create.py
	deleted:    tests/test_views/test_api_objects_drafts_modify.py
	deleted:    tests/test_views/test_api_objects_drafts_publish.py
	deleted:    tests/test_views/test_api_objects_search.py
	deleted:    tests/test_views/test_api_objects_validate.py
	deleted:    tests/test_views/test_api_prefixes_create.py
	deleted:    tests/test_views/test_api_prefixes_token.py
	deleted:    tests/test_views/test_get_object_id_draft.py
	deleted:    tests/test_views/test_get_objectid.py
	deleted:    tests/test_views/test_published_object_by_id.py
	modified:   token.json

* Swagger move (#283)

* Remove API app
Changes to be committed:
	deleted:    api/__init__.py
	deleted:    api/admin.py
	deleted:    api/apps.py
	deleted:    api/fixtures/bootstrap.json
	deleted:    api/fixtures/metafixtures
	deleted:    api/fixtures/metafixtures.json
	deleted:    api/keys.sh
	deleted:    api/migrations/0001_initial.py
	deleted:    api/migrations/0002_auto_20220124_2356.py
	deleted:    api/migrations/0003_rename_meta_table_prefix_table.py
	deleted:    api/migrations/0004_rename_group_info_groupinfo.py
	deleted:    api/migrations/0005_rename_prefixes_prefix.py
	deleted:    api/migrations/0006_delete_new_users.py
	deleted:    api/migrations/__init__.py
	deleted:    api/model/__init__.py
	deleted:    api/model/groups.py
	deleted:    api/model/prefix.py
	deleted:    api/models.py
	deleted:    api/permissions.py
	deleted:    api/rdb.sh
	deleted:    api/request_definitions/GET.schema
	deleted:    api/request_definitions/POST.schema
	deleted:    api/request_definitions/templates/DELETE_delete_object_by_id.schema
	deleted:    api/request_definitions/templates/GET_activate_account.schema
	deleted:    api/request_definitions/templates/GET_get_object_by_id.schema
	deleted:    api/request_definitions/templates/GET_retrieve_available_schema.schema
	deleted:    api/request_definitions/templates/POST_convert_existing_object_between_schemas.schema
	deleted:    api/request_definitions/templates/POST_convert_payload_to_schema.schema
	deleted:    api/request_definitions/templates/POST_new_account.schema
	deleted:    api/request_definitions/templates/POST_object_listing_by_token.schema
	deleted:    api/request_definitions/templates/POST_objects_draft.schema
	deleted:    api/request_definitions/templates/POST_objects_publish.schema
	deleted:    api/request_definitions/templates/POST_read_object.schema
	deleted:    api/request_definitions/templates/POST_validate_payload_against_schema.schema
	deleted:    api/scripts/__init__.py
	deleted:    api/scripts/method_specific/GET_draft_object_by_id.py
	deleted:    api/scripts/method_specific/GET_published_object_by_id.py
	deleted:    api/scripts/method_specific/GET_published_object_by_id_with_version.py
	deleted:    api/scripts/method_specific/GET_retrieve_available_schema.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_create.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_delete.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_modify.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_permissions.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_permissions_set.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_publish.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_read.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_token.py
	deleted:    api/scripts/method_specific/POST_api_objects_publish.py
	deleted:    api/scripts/method_specific/POST_api_objects_published.py
	deleted:    api/scripts/method_specific/POST_api_objects_search.py
	deleted:    api/scripts/method_specific/POST_api_objects_token.py
	deleted:    api/scripts/method_specific/POST_validate_payload_against_schema.py
	deleted:    api/scripts/method_specific/__init__.py
	deleted:    api/scripts/utilities/DbUtils.py
	deleted:    api/scripts/utilities/FileUtils.py
	deleted:    api/scripts/utilities/JsonUtils.py
	deleted:    api/scripts/utilities/RequestUtils.py
	deleted:    api/scripts/utilities/ResponseUtils.py
	deleted:    api/scripts/utilities/SettingsUtils.py
	deleted:    api/scripts/utilities/UserUtils.py
	deleted:    api/scripts/utilities/__init__.py
	deleted:    api/serializers.py
	deleted:    api/signals.py
	deleted:    api/templates/api/account_activation_message.html
	deleted:    api/urls.py
	deleted:    api/validation_definitions/IEEE/2791object.json
	deleted:    api/validation_definitions/IEEE/description_domain.json
	deleted:    api/validation_definitions/IEEE/error_domain.json
	deleted:    api/validation_definitions/IEEE/execution_domain.json
	deleted:    api/validation_definitions/IEEE/io_domain.json
	deleted:    api/validation_definitions/IEEE/parametric_domain.json
	deleted:    api/validation_definitions/IEEE/provenance_domain.json
	deleted:    api/validation_definitions/IEEE/usability_domain.json
	deleted:    api/validation_definitions/IEEE_sub/IEEE2791-2020.schema
	deleted:    api/validation_definitions/IEEE_sub/domains/description_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/error_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/execution_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/io_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/parametric_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/provenance_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/usability_domain.json
	deleted:    api/validation_definitions/uri_external
	deleted:    api/views.py
	new file:   config/settings.py
	modified:   config/urls.py

Changes not staged for commit:
	modified:   authentication/apis.py
	modified:   authentication/migrations/0001_initial.py
	deleted:    authentication/migrations/0002_newuser.py
	modified:   authentication/services.py
	modified:   docs/refactor.md
	modified:   search/selectors.py
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_database.py
	deleted:    tests/test_fixtures.py
	deleted:    tests/test_models
	modified:   tests/test_views/test_api_account_activate.py
	deleted:    tests/test_views/test_api_accounts_describe.py
	modified:   tests/test_views/test_api_auth_add.py
	modified:   tests/test_views/test_api_auth_reset_token.py
	deleted:    tests/test_views/test_api_groups_group_info.py
	deleted:    tests/test_views/test_api_groups_modify.py
	deleted:    tests/test_views/test_api_objects.py
	deleted:    tests/test_views/test_api_objects_drafts_create.py
	deleted:    tests/test_views/test_api_objects_drafts_modify.py
	deleted:    tests/test_views/test_api_objects_drafts_publish.py
	deleted:    tests/test_views/test_api_objects_search.py
	deleted:    tests/test_views/test_api_objects_validate.py
	deleted:    tests/test_views/test_api_prefixes_create.py
	deleted:    tests/test_views/test_api_prefixes_token.py
	deleted:    tests/test_views/test_get_object_id_draft.py
	deleted:    tests/test_views/test_get_objectid.py
	deleted:    tests/test_views/test_published_object_by_id.py
	modified:   token.json

* Framework for BioCompute model

Changes to be committed:
	new file:   biocompute/__init__.py
	new file:   biocompute/admin.py
	new file:   biocompute/apis.py
	new file:   biocompute/migrations/__init__.py
	new file:   biocompute/models.py
	new file:   biocompute/selectors.py
	new file:   biocompute/services.py
	new file:   biocompute/urls.py

* Added files for Prefix model

Changes to be committed:
	new file:   prefix/__init__.py
	new file:   prefix/admin.py
	new file:   prefix/apis.py
	new file:   prefix/apps.py
	new file:   prefix/migrations/__init__.py
	new file:   prefix/models.py
	new file:   prefix/selectors.py
	new file:   prefix/services.py
	new file:   prefix/urls.py

* Tests for authentication

Changes to be committed:
	modified:   .gitignore
	modified:   authentication/apis.py
	modified:   authentication/migrations/0001_initial.py
	deleted:    authentication/migrations/0002_newuser.py
	modified:   authentication/services.py
	new file:   biocompute/migrations/0001_initial.py
	modified:   docs/refactor.md
	new file:   prefix/migrations/0001_initial.py
	modified:   search/selectors.py
	new file:   test.json
	new file:   tests/fixtures/old_test_data.json
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_database.py
	deleted:    tests/test_fixtures.py
	deleted:    tests/test_models
	modified:   tests/test_views/test_api_account_activate.py
	renamed:    tests/test_views/test_api_accounts_describe.py -> tests/test_views/test_api_account_describe.py
	modified:   tests/test_views/test_api_auth_add.py
	modified:   tests/test_views/test_api_auth_reset_token.py
	deleted:    tests/test_views/test_api_groups_group_info.py
	deleted:    tests/test_views/test_api_groups_modify.py
	deleted:    tests/test_views/test_api_objects.py
	deleted:    tests/test_views/test_api_objects_drafts_create.py
	deleted:    tests/test_views/test_api_objects_drafts_modify.py
	deleted:    tests/test_views/test_api_objects_drafts_publish.py
	deleted:    tests/test_views/test_api_objects_search.py
	deleted:    tests/test_views/test_api_objects_validate.py
	deleted:    tests/test_views/test_api_prefixes_create.py
	deleted:    tests/test_views/test_api_prefixes_token.py
	deleted:    tests/test_views/test_get_object_id_draft.py
	deleted:    tests/test_views/test_get_objectid.py
	deleted:    tests/test_views/test_published_object_by_id.py
	modified:   token.json

* Move Swagger files and implement BCO draft create

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	new file:   config/services.py
	modified:   config/urls.py
	modified:   docs/refactor.md
	modified:   prefix/urls.py
	new file:   tests/fixtures/example_bco.py
	new file:   tests/test_views/test_api_objects_drafts_create.py

* Doc fix in Bco.models
Changes to be committed:
	modified:   biocompute/models.py

* Biocompute model (#284)

* Remove API app
Changes to be committed:
	deleted:    api/__init__.py
	deleted:    api/admin.py
	deleted:    api/apps.py
	deleted:    api/fixtures/bootstrap.json
	deleted:    api/fixtures/metafixtures
	deleted:    api/fixtures/metafixtures.json
	deleted:    api/keys.sh
	deleted:    api/migrations/0001_initial.py
	deleted:    api/migrations/0002_auto_20220124_2356.py
	deleted:    api/migrations/0003_rename_meta_table_prefix_table.py
	deleted:    api/migrations/0004_rename_group_info_groupinfo.py
	deleted:    api/migrations/0005_rename_prefixes_prefix.py
	deleted:    api/migrations/0006_delete_new_users.py
	deleted:    api/migrations/__init__.py
	deleted:    api/model/__init__.py
	deleted:    api/model/groups.py
	deleted:    api/model/prefix.py
	deleted:    api/models.py
	deleted:    api/permissions.py
	deleted:    api/rdb.sh
	deleted:    api/request_definitions/GET.schema
	deleted:    api/request_definitions/POST.schema
	deleted:    api/request_definitions/templates/DELETE_delete_object_by_id.schema
	deleted:    api/request_definitions/templates/GET_activate_account.schema
	deleted:    api/request_definitions/templates/GET_get_object_by_id.schema
	deleted:    api/request_definitions/templates/GET_retrieve_available_schema.schema
	deleted:    api/request_definitions/templates/POST_convert_existing_object_between_schemas.schema
	deleted:    api/request_definitions/templates/POST_convert_payload_to_schema.schema
	deleted:    api/request_definitions/templates/POST_new_account.schema
	deleted:    api/request_definitions/templates/POST_object_listing_by_token.schema
	deleted:    api/request_definitions/templates/POST_objects_draft.schema
	deleted:    api/request_definitions/templates/POST_objects_publish.schema
	deleted:    api/request_definitions/templates/POST_read_object.schema
	deleted:    api/request_definitions/templates/POST_validate_payload_against_schema.schema
	deleted:    api/scripts/__init__.py
	deleted:    api/scripts/method_specific/GET_draft_object_by_id.py
	deleted:    api/scripts/method_specific/GET_published_object_by_id.py
	deleted:    api/scripts/method_specific/GET_published_object_by_id_with_version.py
	deleted:    api/scripts/method_specific/GET_retrieve_available_schema.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_create.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_delete.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_modify.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_permissions.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_permissions_set.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_publish.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_read.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_token.py
	deleted:    api/scripts/method_specific/POST_api_objects_publish.py
	deleted:    api/scripts/method_specific/POST_api_objects_published.py
	deleted:    api/scripts/method_specific/POST_api_objects_search.py
	deleted:    api/scripts/method_specific/POST_api_objects_token.py
	deleted:    api/scripts/method_specific/POST_validate_payload_against_schema.py
	deleted:    api/scripts/method_specific/__init__.py
	deleted:    api/scripts/utilities/DbUtils.py
	deleted:    api/scripts/utilities/FileUtils.py
	deleted:    api/scripts/utilities/JsonUtils.py
	deleted:    api/scripts/utilities/RequestUtils.py
	deleted:    api/scripts/utilities/ResponseUtils.py
	deleted:    api/scripts/utilities/SettingsUtils.py
	deleted:    api/scripts/utilities/UserUtils.py
	deleted:    api/scripts/utilities/__init__.py
	deleted:    api/serializers.py
	deleted:    api/signals.py
	deleted:    api/templates/api/account_activation_message.html
	deleted:    api/urls.py
	deleted:    api/validation_definitions/IEEE/2791object.json
	deleted:    api/validation_definitions/IEEE/description_domain.json
	deleted:    api/validation_definitions/IEEE/error_domain.json
	deleted:    api/validation_definitions/IEEE/execution_domain.json
	deleted:    api/validation_definitions/IEEE/io_domain.json
	deleted:    api/validation_definitions/IEEE/parametric_domain.json
	deleted:    api/validation_definitions/IEEE/provenance_domain.json
	deleted:    api/validation_definitions/IEEE/usability_domain.json
	deleted:    api/validation_definitions/IEEE_sub/IEEE2791-2020.schema
	deleted:    api/validation_definitions/IEEE_sub/domains/description_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/error_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/execution_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/io_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/parametric_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/provenance_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/usability_domain.json
	deleted:    api/validation_definitions/uri_external
	deleted:    api/views.py
	new file:   config/settings.py
	modified:   config/urls.py

Changes not staged for commit:
	modified:   authentication/apis.py
	modified:   authentication/migrations/0001_initial.py
	deleted:    authentication/migrations/0002_newuser.py
	modified:   authentication/services.py
	modified:   docs/refactor.md
	modified:   search/selectors.py
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_database.py
	deleted:    tests/test_fixtures.py
	deleted:    tests/test_models
	modified:   tests/test_views/test_api_account_activate.py
	deleted:    tests/test_views/test_api_accounts_describe.py
	modified:   tests/test_views/test_api_auth_add.py
	modified:   tests/test_views/test_api_auth_reset_token.py
	deleted:    tests/test_views/test_api_groups_group_info.py
	deleted:    tests/test_views/test_api_groups_modify.py
	deleted:    tests/test_views/test_api_objects.py
	deleted:    tests/test_views/test_api_objects_drafts_create.py
	deleted:    tests/test_views/test_api_objects_drafts_modify.py
	deleted:    tests/test_views/test_api_objects_drafts_publish.py
	deleted:    tests/test_views/test_api_objects_search.py
	deleted:    tests/test_views/test_api_objects_validate.py
	deleted:    tests/test_views/test_api_prefixes_create.py
	deleted:    tests/test_views/test_api_prefixes_token.py
	deleted:    tests/test_views/test_get_object_id_draft.py
	deleted:    tests/test_views/test_get_objectid.py
	deleted:    tests/test_views/test_published_object_by_id.py
	modified:   token.json

* Framework for BioCompute model

Changes to be committed:
	new file:   biocompute/__init__.py
	new file:   biocompute/admin.py
	new file:   biocompute/apis.py
	new file:   biocompute/migrations/__init__.py
	new file:   biocompute/models.py
	new file:   biocompute/selectors.py
	new file:   biocompute/services.py
	new file:   biocompute/urls.py

* Added files for Prefix model

Changes to be committed:
	new file:   prefix/__init__.py
	new file:   prefix/admin.py
	new file:   prefix/apis.py
	new file:   prefix/apps.py
	new file:   prefix/migrations/__init__.py
	new file:   prefix/models.py
	new file:   prefix/selectors.py
	new file:   prefix/services.py
	new file:   prefix/urls.py

* Tests for authentication

Changes to be committed:
	modified:   .gitignore
	modified:   authentication/apis.py
	modified:   authentication/migrations/0001_initial.py
	deleted:    authentication/migrations/0002_newuser.py
	modified:   authentication/services.py
	new file:   biocompute/migrations/0001_initial.py
	modified:   docs/refactor.md
	new file:   prefix/migrations/0001_initial.py
	modified:   search/selectors.py
	new file:   test.json
	new file:   tests/fixtures/old_test_data.json
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_database.py
	deleted:    tests/test_fixtures.py
	deleted:    tests/test_models
	modified:   tests/test_views/test_api_account_activate.py
	renamed:    tests/test_views/test_api_accounts_describe.py -> tests/test_views/test_api_account_describe.py
	modified:   tests/test_views/test_api_auth_add.py
	modified:   tests/test_views/test_api_auth_reset_token.py
	deleted:    tests/test_views/test_api_groups_group_info.py
	deleted:    tests/test_views/test_api_groups_modify.py
	deleted:    tests/test_views/test_api_objects.py
	deleted:    tests/test_views/test_api_objects_drafts_create.py
	deleted:    tests/test_views/test_api_objects_drafts_modify.py
	deleted:    tests/test_views/test_api_objects_drafts_publish.py
	deleted:    tests/test_views/test_api_objects_search.py
	deleted:    tests/test_views/test_api_objects_validate.py
	deleted:    tests/test_views/test_api_prefixes_create.py
	deleted:    tests/test_views/test_api_prefixes_token.py
	deleted:    tests/test_views/test_get_object_id_draft.py
	deleted:    tests/test_views/test_get_objectid.py
	deleted:    tests/test_views/test_published_object_by_id.py
	modified:   token.json

* Move Swagger files and implement BCO draft create

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	new file:   config/services.py
	modified:   config/urls.py
	modified:   docs/refactor.md
	modified:   prefix/urls.py
	new file:   tests/fixtures/example_bco.py
	new file:   tests/test_views/test_api_objects_drafts_create.py

* Doc fix in Bco.models
Changes to be committed:
	modified:   biocompute/models.py

* Updated biocompute.model and prefix.model

Added the DraftsCreateApi and tests.
This included serializers for BCO creation
Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/services.py
	modified:   config/services.py
	modified:   prefix/models.py
	modified:   prefix/services.py
	modified:   test.json
	modified:   tests/fixtures/test_data.json
	new file:   tests/test_views/test_api_objects_drafts_create.py

* Implemented PrefixesCreateApi

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   config/fixtures/local_data.json
	modified:   config/services.py
	modified:   config/urls.py
	modified:   prefix/apis.py
	modified:   prefix/services.py
	modified:   prefix/urls.py
	modified:   search/apis.py
	modified:   tests/test_views/test_api_auth_remove.py
	modified:   tests/test_views/test_api_objects_drafts_create.py
	new file:   tests/test_views/test_api_prefixes_create.py

* Added Prefix management URLs and APIs

Changes to be committed:
	modified:   config/fixtures/local_data.json
	modified:   docs/refactor.md
	modified:   prefix/apis.py
	modified:   prefix/services.py
	modified:   prefix/urls.py
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_views/test_api_prefixes_create.py
	new file:   tests/test_views/test_prefixes_create.py
	new file:   tests/test_views/test_prefixes_modify.py

* Cleaning up some things
Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/migrations/0001_initial.py
	modified:   prefix/apis.py
	modified:   prefix/migrations/0001_initial.py
	new file:   tests/test_views/test_account_activate.py
	new file:   tests/test_views/test_account_describe.py
	new file:   tests/test_views/test_account_new.py
	new file:   tests/test_views/test_auth_add.py
	new file:   tests/test_views/test_auth_remove.py
	new file:   tests/test_views/test_auth_reset_token.py
	new file:   tests/test_views/test_objects_drafts_create.py

* Add prefix creation function
Changes to be committed:
	modified:   authentication/services.py
	modified:   biocompute/models.py
	modified:   config/settings.py
	modified:   docs/refactor.md
	modified:   prefix/apis.py
	modified:   prefix/models.py
	modified:   prefix/services.py
	modified:   tests/test_views/test_api_objects_drafts_create.py

* Add Prefix Modify API endpoint
On branch prefix_perms
Your branch is up to date with 'origin/prefix_perms'.

Changes to be committed:
	modified:   config/services.py
	modified:   prefix/apis.py
	modified:   prefix/models.py
	modified:   prefix/selectors.py
	modified:   prefix/services.py

* response_c

* Add `DraftRetrieveApi`

To do this functions related to Prefixes and the associated permissions were created

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   biocompute/selectors.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	modified:   config/asgi.py
	modified:   config/fixtures/local_data.json
	modified:   config/services.py
	modified:   config/urls.py
	modified:   prefix/selectors.py
	modified:   prefix/services.py
	deleted:    test.json
	modified:   tests/fixtures/example_bco.py
	modified:   tests/fixtures/test_data.json
	deleted:    token.json

* Update testing functions

Created subdirectory and moved test functions
Changes to be committed:
	renamed:    tests/test_views/__init__.py -> tests/test_apis/__init__.py
	new file:   tests/test_apis/test_api_authentication/__init__.py
	renamed:    tests/test_views/test_account_activate.py -> tests/test_apis/test_api_authentication/test_account_activate.py
	renamed:    tests/test_views/test_account_describe.py -> tests/test_apis/test_api_authentication/test_account_describe.py
	renamed:    tests/test_views/test_account_new.py -> tests/test_apis/test_api_authentication/test_account_new.py
	renamed:    tests/test_views/test_api_auth_add.py -> tests/test_apis/test_api_authentication/test_api_auth_add.py
	renamed:    tests/test_views/test_api_auth_remove.py -> tests/test_apis/test_api_authentication/test_api_auth_remove.py
	renamed:    tests/test_views/test_api_auth_reset_token.py -> tests/test_apis/test_api_authentication/test_api_auth_reset_token.py
	renamed:    tests/test_views/test_api_objects_drafts_create.py -> tests/test_apis/test_api_objects_drafts_create.py
	renamed:    tests/test_views/test_auth_add.py -> tests/test_apis/test_auth_add.py
	renamed:    tests/test_views/test_auth_remove.py -> tests/test_apis/test_auth_remove.py
	renamed:    tests/test_views/test_auth_reset_token.py -> tests/test_apis/test_auth_reset_token.py
	renamed:    tests/test_views/test_objects_drafts_create.py -> tests/test_apis/test_objects_drafts_create.py
	renamed:    tests/test_views/test_prefixes_create.py -> tests/test_apis/test_prefixes_create.py
	new file:   tests/test_apis/test_prefixes_modify.py
	deleted:    tests/test_views/test_api_account_activate.py
	deleted:    tests/test_views/test_api_account_describe.py
	deleted:    tests/test_views/test_api_account_new.py
	deleted:    tests/test_views/test_prefixes_modify.py

* Add `DraftRetrieveApi`

To do this functions related to Prefixes and the associated permissions were created

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   biocompute/selectors.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	modified:   config/asgi.py
	modified:   config/fixtures/local_data.json
	modified:   config/services.py
	modified:   config/urls.py
	modified:   prefix/selectors.py
	modified:   prefix/services.py
	deleted:    test.json
	modified:   tests/fixtures/example_bco.py
	modified:   tests/fixtures/test_data.json
	deleted:    token.json

* Update testing functions

Created subdirectory and moved test functions
Changes to be committed:
	renamed:    tests/test_views/__init__.py -> tests/test_apis/__init__.py
	new file:   tests/test_apis/test_api_authentication/__init__.py
	renamed:    tests/test_views/test_account_activate.py -> tests/test_apis/test_api_authentication/test_account_activate.py
	renamed:    tests/test_views/test_account_describe.py -> tests/test_apis/test_api_authentication/test_account_describe.py
	renamed:    tests/test_views/test_account_new.py -> tests/test_apis/test_api_authentication/test_account_new.py
	renamed:    tests/test_views/test_api_auth_add.py -> tests/test_apis/test_api_authentication/test_api_auth_add.py
	renamed:    tests/test_views/test_api_auth_remove.py -> tests/test_apis/test_api_authentication/test_api_auth_remove.py
	renamed:    tests/test_views/test_api_auth_reset_token.py -> tests/test_apis/test_api_authentication/test_api_auth_reset_token.py
	renamed:    tests/test_views/test_api_objects_drafts_create.py -> tests/test_apis/test_api_objects_drafts_create.py
	renamed:    tests/test_views/test_auth_add.py -> tests/test_apis/test_auth_add.py
	renamed:    tests/test_views/test_auth_remove.py -> tests/test_apis/test_auth_remove.py
	renamed:    tests/test_views/test_auth_reset_token.py -> tests/test_apis/test_auth_reset_token.py
	renamed:    tests/test_views/test_objects_drafts_create.py -> tests/test_apis/test_objects_drafts_create.py
	renamed:    tests/test_views/test_prefixes_create.py -> tests/test_apis/test_prefixes_create.py
	new file:   tests/test_apis/test_prefixes_modify.py
	deleted:    tests/test_views/test_api_account_activate.py
	deleted:    tests/test_views/test_api_account_describe.py
	deleted:    tests/test_views/test_api_account_new.py
	deleted:    tests/test_views/test_prefixes_modify.py

* Update to Test functions

Changes to be committed:
	modified:   biocompute/migrations/0001_initial.py
	modified:   docs/refactor.md
	modified:   prefix/apis.py
	modified:   prefix/migrations/0001_initial.py
	modified:   prefix/services.py
	new file:   tests/fixtures/bco_dump.json
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_apis/test_api_authentication/test_api_auth_add.py
	deleted:    tests/test_apis/test_api_authentication/test_api_auth_reset_token.py
	renamed:    tests/test_apis/test_auth_add.py -> tests/test_apis/test_api_authentication/test_auth_add.py
	renamed:    tests/test_apis/test_auth_reset_token.py -> tests/test_apis/test_api_authentication/test_auth_reset_token.py
	renamed:    tests/test_apis/test_api_authentication/test_api_auth_remove.py -> tests/test_apis/test_api_authentication/testi_auth_remove.py
	deleted:    tests/test_apis/test_api_objects_drafts_create.py
	new file:   tests/test_apis/test_api_prefix/__init__.py
	renamed:    tests/test_apis/test_prefixes_create.py -> tests/test_apis/test_api_prefix/test_prefixes_create.py
	renamed:    tests/test_apis/test_prefixes_modify.py -> tests/test_apis/test_api_prefix/test_prefixes_modify.py
	deleted:    tests/test_apis/test_auth_remove.py
	new file:   tests/test_apis/test_biocompute/__init__.py
	renamed:    tests/test_apis/test_objects_drafts_create.py -> tests/test_apis/test_biocompute/test_objects_drafts_create.py

* Bco perms (#293)

* Add `DraftRetrieveApi`

To do this functions related to Prefixes and the associated permissions were created

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   biocompute/selectors.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	modified:   config/asgi.py
	modified:   config/fixtures/local_data.json
	modified:   config/services.py
	modified:   config/urls.py
	modified:   prefix/selectors.py
	modified:   prefix/services.py
	deleted:    test.json
	modified:   tests/fixtures/example_bco.py
	modified:   tests/fixtures/test_data.json
	deleted:    token.json

* Update testing functions

Created subdirectory and moved test functions
Changes to be committed:
	renamed:    tests/test_views/__init__.py -> tests/test_apis/__init__.py
	new file:   tests/test_apis/test_api_authentication/__init__.py
	renamed:    tests/test_views/test_account_activate.py -> tests/test_apis/test_api_authentication/test_account_activate.py
	renamed:    tests/test_views/test_account_describe.py -> tests/test_apis/test_api_authentication/test_account_describe.py
	renamed:    tests/test_views/test_account_new.py -> tests/test_apis/test_api_authentication/test_account_new.py
	renamed:    tests/test_views/test_api_auth_add.py -> tests/test_apis/test_api_authentication/test_api_auth_add.py
	renamed:    tests/test_views/test_api_auth_remove.py -> tests/test_apis/test_api_authentication/test_api_auth_remove.py
	renamed:    tests/test_views/test_api_auth_reset_token.py -> tests/test_apis/test_api_authentication/test_api_auth_reset_token.py
	renamed:    tests/test_views/test_api_objects_drafts_create.py -> tests/test_apis/test_api_objects_drafts_create.py
	renamed:    tests/test_views/test_auth_add.py -> tests/test_apis/test_auth_add.py
	renamed:    tests/test_views/test_auth_remove.py -> tests/test_apis/test_auth_remove.py
	renamed:    tests/test_views/test_auth_reset_token.py -> tests/test_apis/test_auth_reset_token.py
	renamed:    tests/test_views/test_objects_drafts_create.py -> tests/test_apis/test_objects_drafts_create.py
	renamed:    tests/test_views/test_prefixes_create.py -> tests/test_apis/test_prefixes_create.py
	new file:   tests/test_apis/test_prefixes_modify.py
	deleted:    tests/test_views/test_api_account_activate.py
	deleted:    tests/test_views/test_api_account_describe.py
	deleted:    tests/test_views/test_api_account_new.py
	deleted:    tests/test_views/test_prefixes_modify.py

* Update to Test functions

Changes to be committed:
	modified:   biocompute/migrations/0001_initial.py
	modified:   docs/refactor.md
	modified:   prefix/apis.py
	modified:   prefix/migrations/0001_initial.py
	modified:   prefix/services.py
	new file:   tests/fixtures/bco_dump.json
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_apis/test_api_authentication/test_api_auth_add.py
	deleted:    tests/test_apis/test_api_authentication/test_api_auth_reset_token.py
	renamed:    tests/test_apis/test_auth_add.py -> tests/test_apis/test_api_authentication/test_auth_add.py
	renamed:    tests/test_apis/test_auth_reset_token.py -> tests/test_apis/test_api_authentication/test_auth_reset_token.py
	renamed:    tests/test_apis/test_api_authentication/test_api_auth_remove.py -> tests/test_apis/test_api_authentication/testi_auth_remove.py
	deleted:    tests/test_apis/test_api_objects_drafts_create.py
	new file:   tests/test_apis/test_api_prefix/__init__.py
	renamed:    tests/test_apis/test_prefixes_create.py -> tests/test_apis/test_api_prefix/test_prefixes_create.py
	renamed:    tests/test_apis/test_prefixes_modify.py -> tests/test_apis/test_api_prefix/test_prefixes_modify.py
	deleted:    tests/test_apis/test_auth_remove.py
	new file:   tests/test_apis/test_biocompute/__init__.py
	renamed:    tests/test_apis/test_objects_drafts_create.py -> tests/test_apis/test_biocompute/test_objects_drafts_create.py

* Add `access_count` incrementer to DraftRetrieveApi

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/services.py
	modified:   prefix/services.py

* Added PublishedRetrieveApi class
Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/selectors.py
	modified:   config/urls.py

* Update test DB and testing functions

Changes to be committed:
	modified:   config/fixtures/local_data.json
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_apis/test_api_objects_drafts_create.py
	deleted:    tests/test_apis/test_auth_add.py
	deleted:    tests/test_apis/test_auth_remove.py
	deleted:    tests/test_apis/test_auth_reset_token.py
	renamed:    tests/test_apis/test_objects_drafts_create.py -> tests/test_apis/test_biocompute/objects_drafts_create.py
	deleted:    tests/test_apis/test_prefixes_create.py
	deleted:    tests/test_apis/test_prefixes_modify.py

* Add DraftsModifyApi

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/selectors.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	modified:   prefix/selectors.py
	deleted:    tests/test_apis/test_biocompute/objects_drafts_create.py
	deleted:    tests/test_apis/test_biocompute/test_objects_drafts_create.py

* test for objects_drafts_create

Changes to be committed:
	new file:   tests/test_apis/test_biocompute/test_objects_drafts_create.py

* split("/")

* Publish draft (#308)

* Add DraftsModifyApi

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/selectors.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	modified:   prefix/selectors.py
	deleted:    tests/test_apis/test_biocompute/objects_drafts_create.py
	deleted:    tests/test_apis/test_biocompute/test_objects_drafts_create.py

* Add IEEE schema
Changes to be committed:
	new file:   .secrets
	new file:   config/IEEE/2791object.json
	new file:   config/IEEE/description_domain.json
	new file:   config/IEEE/error_domain.json
	new file:   config/IEEE/execution_domain.json
	new file:   config/IEEE/io_domain.json
	new file:   config/IEEE/parametric_domain.json
	new file:   config/IEEE/provenance_domain.json
	new file:   config/IEEE/usability_domain.json

* test_objects_drafts_create
Changes to be committed:
	new file:   tests/test_apis/test_biocompute/test_objects_drafts_create.py

* Fix test
Changes to be committed:
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_create.py

* Enable publish bco endpoint

This included a great many supporting functions
and permission checks to accomplish. Also added
the validate functions to the codebase

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/selectors.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	modified:   config/services.py
	modified:   docs/refactor.md
	modified:   prefix/selectors.py
	new file:   tests/test_apis/test_biocompute/test_objects_drafts_publish.py

* Add BCO Score to model.

Also added functions and methods for BCO Score.
Updates to the BCO admin panel.
Updates to the `test_data.json` and `local_data.json`
Fix # 310
Changes to be committed:
	modified:   authentication/migrations/0001_initial.py
	modified:   biocompute/admin.py
	modified:   biocompute/apis.py
	modified:   biocompute/migrations/0001_initial.py
	modified:   biocompute/models.py
	modified:   biocompute/services.py
	new file:   config/bco_scores.py
	modified:   config/fixtures/local_data.json
	modified:   tests/fixtures/test_data.json

* Add BCODB search API endpoint.

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   search/apis.py
	modified:   search/selectors.py
	modified:   search/urls.py

* Add POST search
Changes to be committed:
	modified:   authentication/apis.py
	modified:   search/apis.py

* Updated config file to `.secrets`

also updated accounts/describe
Changes to be committed:
	modified:   .gitignore
	new file:   .secrets.example
	modified:   authentication/selectors.py
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   biocompute/selectors.py
	modified:   config/settings.py
	deleted:    server.conf
	deleted:    sever.conf.example

* Fix config/urls.py error
Changes to be committed:
	deleted:    .secrets
	modified:   config/settings.py
	modified:   config/urls.py

* Refactor `config/services.py::response_constructor`
Changes to be committed:
	modified:   config/services.py
	modified:   tests/test_apis/test_api_prefix/test_prefixes_create.py

* Prefix registry (#318)

* Created test_objects_drafts_modify, hasn't passed test yet

* Created test_objects_drafts_modify, hasn't passed test yet

* Created test_objects_drafts_modify, hasn't passed test yet

* new tests

* Update modify_prefix permissions
Changes to be committed:
	modified:   authentication/selectors.py
	modified:   config/fixtures/local_data.json
	modified:   prefix/services.py

* Created and tested test_objects_drafts_modify API

* Fixes for Prefix creation

Changes to be committed:
	modified:   config/services.py
	modified:   prefix/apis.py
	modified:   tests/test_apis/test_api_prefix/test_prefixes_create.py

* Add UserSearch endpoint

Changes to be committed:
	modified:   prefix/apis.py
	modified:   prefix/selectors.py
	modified:   search/apis.py
	modified:   search/urls.py

* Fixes for deployment

 Changes to be committed:
	modified:   .secrets.example
	modified:   admin_only/bco_api.service
	modified:   biocompute/apis.py
	modified:   config/fixtures/test_portal.json
	modified:   config/settings.py
	modified:   tests/fixtures/test_data.json
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_create.py

* test_objects_drafts_publish failed. Kicking back to Hadley for more investigation

* Update bco_api.conf

Changes to be committed:
	modified:   admin_only/bco_api.conf

---------

Co-authored-by: tianywan819 <[email protected]>
Co-authored-by: acoleman29 <[email protected]>

* Fixes for testing files

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/services.py
	modified:   config/bco_scores.py
	modified:   config/services.py
	modified:   config/settings.py
	modified:   config/urls.py
	modified:   tests/fixtures/test_data.json
	renamed:    tests/fixtures/example_bco.py -> tests/fixtures/testing_bcos.py
	modified:   tests/test_apis/test_api_prefix/test_prefixes_create.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_modify.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_publish.py

* "derrived_from": []

* fix test

* Add Validate url endpoint

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/urls.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_create.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_publish.py

* Update create test to include HOSTNAME

Changes to be committed:
	modified:   config/services.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_create.py

* Rollback status for validation

Changes to be committed:
	modified:   biocompute/apis.py

* Changes to be committed:
	modified:   biocompute/apis.py

* Typo fix
Changes to be committed:
	modified:   biocompute/apis.py

* Add `test_portal.json` for testing

Changes to be committed:
	modified:   config/fixtures/test_portal.json

* Testing fixes

Changes to be committed:
	modified:   admin_only/bco_api.conf
	modified:   config/fixtures/test_portal.json

* Fix for draft publish

Changes to be committed:
	modified:   config/services.py

* Add new_bco_instance.save()

Changes to be committed:
	modified:   biocompute/services.py
	modified:   config/services.py

* CustomJSONWebTokenAuthentication for GET Pub BCO
Changes to be committed:
	modified:   biocompute/apis.py

* Updates to authentication.apis.py
Changes to be committed:
	modified:   authentication/apis.py
	modified:   authentication/services.py
	modified:   search/apis.py

* Updates to biocompute.apis.py

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/selectors.py
	modified:   search/apis.py
	modified:   tests/fixtures/testing_bcos.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_create.py

* Remove print statements

Changes to be committed:
	modified:   authentication/apis.py
	modified:   authentication/services.py
	modified:   authentication/urls.py
	modified:   biocompute/apis.py
	modified:   biocompute/services.py
	modified:   config/urls.py
	modified:   prefix/services.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_publish.py

* Updates to prefix.apis

Changes to be committed:
	modified:   prefix/apis.py

* print(

* change publish bco rejected response

On branch docs
Your branch is up to date with 'origin/docs'.

---------

Co-authored-by: tianywan819 <[email protected]>
Co-authored-by: acoleman29 <[email protected]>
@HadleyKing HadleyKing mentioned this pull request May 20, 2024
Merged
HadleyKing added a commit that referenced this pull request May 20, 2024
@HadleyKing @tianywan819 @acoleman2000
Model refactor (#280)
bf83d8a 
* Change `bcodb` directory to `config` directory

Changes to be committed:
	modified:   .gitignore
	deleted:    bcodb/settings.py
	renamed:    bcodb/__init__.py -> config/__init__.py
	renamed:    bcodb/asgi.py -> config/asgi.py
	renamed:    bcodb/fixtures/local_data.json -> config/fixtures/local_data.json
	renamed:    bcodb/fixtures/test_portal.json -> config/fixtures/test_portal.json
	renamed:    bcodb/urls.py -> config/urls.py
	renamed:    bcodb/wsgi.py -> config/wsgi.py
	modified:   manage.py

* Create NewUser model and remove new_user model

changed model behind `/api/accounts/new/`
Changes to be committed:
	modified:   api/admin.py
	new file:   api/migrations/0006_delete_new_users.py
	modified:   api/models.py
	deleted:    api/scripts/method_specific/POST_api_accounts_new.py
	modified:   api/urls.py
	modified:   api/views.py
	modified:   authentication/admin.py
	modified:   authentication/apis.py
	new file:   authentication/migrations/0002_newuser.py
	modified:   authentication/models.py
	modified:   authentication/selectors.py
	modified:   authentication/services.py
	modified:   tests/fixtures/test_data.json
	modified:   tests/test_views/test_api_account_activate.py
	modified:   tests/test_views/test_api_account_new.py

* Add example values to test account request

Changes to be committed:
	modified:   authentication/apis.py
	new file:   docs/refactor.md

* Account activation has been enabled.

On branch account_authorization
Changes to be committed:
	modified:   api/urls.py
	modified:   api/views.py
	modified:   authentication/apis.py
	modified:   authentication/selectors.py
	modified:   authentication/services.py
	modified:   authentication/urls.py

* Account authorization (#277)

* Account activation has been enabled.

On branch account_authorization
Changes to be committed:
	modified:   api/urls.py
	modified:   api/views.py
	modified:   authentication/apis.py
	modified:   authentication/selectors.py
	modified:   authentication/services.py
	modified:   authentication/urls.py

* get_new_user

* Remove API app
Changes to be committed:
	deleted:    api/__init__.py
	deleted:    api/admin.py
	deleted:    api/apps.py
	deleted:    api/fixtures/bootstrap.json
	deleted:    api/fixtures/metafixtures
	deleted:    api/fixtures/metafixtures.json
	deleted:    api/keys.sh
	deleted:    api/migrations/0001_initial.py
	deleted:    api/migrations/0002_auto_20220124_2356.py
	deleted:    api/migrations/0003_rename_meta_table_prefix_table.py
	deleted:    api/migrations/0004_rename_group_info_groupinfo.py
	deleted:    api/migrations/0005_rename_prefixes_prefix.py
	deleted:    api/migrations/0006_delete_new_users.py
	deleted:    api/migrations/__init__.py
	deleted:    api/model/__init__.py
	deleted:    api/model/groups.py
	deleted:    api/model/prefix.py
	deleted:    api/models.py
	deleted:    api/permissions.py
	deleted:    api/rdb.sh
	deleted:    api/request_definitions/GET.schema
	deleted:    api/request_definitions/POST.schema
	deleted:    api/request_definitions/templates/DELETE_delete_object_by_id.schema
	deleted:    api/request_definitions/templates/GET_activate_account.schema
	deleted:    api/request_definitions/templates/GET_get_object_by_id.schema
	deleted:    api/request_definitions/templates/GET_retrieve_available_schema.schema
	deleted:    api/request_definitions/templates/POST_convert_existing_object_between_schemas.schema
	deleted:    api/request_definitions/templates/POST_convert_payload_to_schema.schema
	deleted:    api/request_definitions/templates/POST_new_account.schema
	deleted:    api/request_definitions/templates/POST_object_listing_by_token.schema
	deleted:    api/request_definitions/templates/POST_objects_draft.schema
	deleted:    api/request_definitions/templates/POST_objects_publish.schema
	deleted:    api/request_definitions/templates/POST_read_object.schema
	deleted:    api/request_definitions/templates/POST_validate_payload_against_schema.schema
	deleted:    api/scripts/__init__.py
	deleted:    api/scripts/method_specific/GET_draft_object_by_id.py
	deleted:    api/scripts/method_specific/GET_published_object_by_id.py
	deleted:    api/scripts/method_specific/GET_published_object_by_id_with_version.py
	deleted:    api/scripts/method_specific/GET_retrieve_available_schema.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_create.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_delete.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_modify.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_permissions.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_permissions_set.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_publish.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_read.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_token.py
	deleted:    api/scripts/method_specific/POST_api_objects_publish.py
	deleted:    api/scripts/method_specific/POST_api_objects_published.py
	deleted:    api/scripts/method_specific/POST_api_objects_search.py
	deleted:    api/scripts/method_specific/POST_api_objects_token.py
	deleted:    api/scripts/method_specific/POST_validate_payload_against_schema.py
	deleted:    api/scripts/method_specific/__init__.py
	deleted:    api/scripts/utilities/DbUtils.py
	deleted:    api/scripts/utilities/FileUtils.py
	deleted:    api/scripts/utilities/JsonUtils.py
	deleted:    api/scripts/utilities/RequestUtils.py
	deleted:    api/scripts/utilities/ResponseUtils.py
	deleted:    api/scripts/utilities/SettingsUtils.py
	deleted:    api/scripts/utilities/UserUtils.py
	deleted:    api/scripts/utilities/__init__.py
	deleted:    api/serializers.py
	deleted:    api/signals.py
	deleted:    api/templates/api/account_activation_message.html
	deleted:    api/urls.py
	deleted:    api/validation_definitions/IEEE/2791object.json
	deleted:    api/validation_definitions/IEEE/description_domain.json
	deleted:    api/validation_definitions/IEEE/error_domain.json
	deleted:    api/validation_definitions/IEEE/execution_domain.json
	deleted:    api/validation_definitions/IEEE/io_domain.json
	deleted:    api/validation_definitions/IEEE/parametric_domain.json
	deleted:    api/validation_definitions/IEEE/provenance_domain.json
	deleted:    api/validation_definitions/IEEE/usability_domain.json
	deleted:    api/validation_definitions/IEEE_sub/IEEE2791-2020.schema
	deleted:    api/validation_definitions/IEEE_sub/domains/description_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/error_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/execution_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/io_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/parametric_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/provenance_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/usability_domain.json
	deleted:    api/validation_definitions/uri_external
	deleted:    api/views.py
	new file:   config/settings.py
	modified:   config/urls.py

Changes not staged for commit:
	modified:   authentication/apis.py
	modified:   authentication/migrations/0001_initial.py
	deleted:    authentication/migrations/0002_newuser.py
	modified:   authentication/services.py
	modified:   docs/refactor.md
	modified:   search/selectors.py
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_database.py
	deleted:    tests/test_fixtures.py
	deleted:    tests/test_models
	modified:   tests/test_views/test_api_account_activate.py
	deleted:    tests/test_views/test_api_accounts_describe.py
	modified:   tests/test_views/test_api_auth_add.py
	modified:   tests/test_views/test_api_auth_reset_token.py
	deleted:    tests/test_views/test_api_groups_group_info.py
	deleted:    tests/test_views/test_api_groups_modify.py
	deleted:    tests/test_views/test_api_objects.py
	deleted:    tests/test_views/test_api_objects_drafts_create.py
	deleted:    tests/test_views/test_api_objects_drafts_modify.py
	deleted:    tests/test_views/test_api_objects_drafts_publish.py
	deleted:    tests/test_views/test_api_objects_search.py
	deleted:    tests/test_views/test_api_objects_validate.py
	deleted:    tests/test_views/test_api_prefixes_create.py
	deleted:    tests/test_views/test_api_prefixes_token.py
	deleted:    tests/test_views/test_get_object_id_draft.py
	deleted:    tests/test_views/test_get_objectid.py
	deleted:    tests/test_views/test_published_object_by_id.py
	modified:   token.json

* Framework for BioCompute model

Changes to be committed:
	new file:   biocompute/__init__.py
	new file:   biocompute/admin.py
	new file:   biocompute/apis.py
	new file:   biocompute/migrations/__init__.py
	new file:   biocompute/models.py
	new file:   biocompute/selectors.py
	new file:   biocompute/services.py
	new file:   biocompute/urls.py

* Added files for Prefix model

Changes to be committed:
	new file:   prefix/__init__.py
	new file:   prefix/admin.py
	new file:   prefix/apis.py
	new file:   prefix/apps.py
	new file:   prefix/migrations/__init__.py
	new file:   prefix/models.py
	new file:   prefix/selectors.py
	new file:   prefix/services.py
	new file:   prefix/urls.py

* Tests for authentication

Changes to be committed:
	modified:   .gitignore
	modified:   authentication/apis.py
	modified:   authentication/migrations/0001_initial.py
	deleted:    authentication/migrations/0002_newuser.py
	modified:   authentication/services.py
	new file:   biocompute/migrations/0001_initial.py
	modified:   docs/refactor.md
	new file:   prefix/migrations/0001_initial.py
	modified:   search/selectors.py
	new file:   test.json
	new file:   tests/fixtures/old_test_data.json
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_database.py
	deleted:    tests/test_fixtures.py
	deleted:    tests/test_models
	modified:   tests/test_views/test_api_account_activate.py
	renamed:    tests/test_views/test_api_accounts_describe.py -> tests/test_views/test_api_account_describe.py
	modified:   tests/test_views/test_api_auth_add.py
	modified:   tests/test_views/test_api_auth_reset_token.py
	deleted:    tests/test_views/test_api_groups_group_info.py
	deleted:    tests/test_views/test_api_groups_modify.py
	deleted:    tests/test_views/test_api_objects.py
	deleted:    tests/test_views/test_api_objects_drafts_create.py
	deleted:    tests/test_views/test_api_objects_drafts_modify.py
	deleted:    tests/test_views/test_api_objects_drafts_publish.py
	deleted:    tests/test_views/test_api_objects_search.py
	deleted:    tests/test_views/test_api_objects_validate.py
	deleted:    tests/test_views/test_api_prefixes_create.py
	deleted:    tests/test_views/test_api_prefixes_token.py
	deleted:    tests/test_views/test_get_object_id_draft.py
	deleted:    tests/test_views/test_get_objectid.py
	deleted:    tests/test_views/test_published_object_by_id.py
	modified:   token.json

* Swagger move (#283)

* Remove API app
Changes to be committed:
	deleted:    api/__init__.py
	deleted:    api/admin.py
	deleted:    api/apps.py
	deleted:    api/fixtures/bootstrap.json
	deleted:    api/fixtures/metafixtures
	deleted:    api/fixtures/metafixtures.json
	deleted:    api/keys.sh
	deleted:    api/migrations/0001_initial.py
	deleted:    api/migrations/0002_auto_20220124_2356.py
	deleted:    api/migrations/0003_rename_meta_table_prefix_table.py
	deleted:    api/migrations/0004_rename_group_info_groupinfo.py
	deleted:    api/migrations/0005_rename_prefixes_prefix.py
	deleted:    api/migrations/0006_delete_new_users.py
	deleted:    api/migrations/__init__.py
	deleted:    api/model/__init__.py
	deleted:    api/model/groups.py
	deleted:    api/model/prefix.py
	deleted:    api/models.py
	deleted:    api/permissions.py
	deleted:    api/rdb.sh
	deleted:    api/request_definitions/GET.schema
	deleted:    api/request_definitions/POST.schema
	deleted:    api/request_definitions/templates/DELETE_delete_object_by_id.schema
	deleted:    api/request_definitions/templates/GET_activate_account.schema
	deleted:    api/request_definitions/templates/GET_get_object_by_id.schema
	deleted:    api/request_definitions/templates/GET_retrieve_available_schema.schema
	deleted:    api/request_definitions/templates/POST_convert_existing_object_between_schemas.schema
	deleted:    api/request_definitions/templates/POST_convert_payload_to_schema.schema
	deleted:    api/request_definitions/templates/POST_new_account.schema
	deleted:    api/request_definitions/templates/POST_object_listing_by_token.schema
	deleted:    api/request_definitions/templates/POST_objects_draft.schema
	deleted:    api/request_definitions/templates/POST_objects_publish.schema
	deleted:    api/request_definitions/templates/POST_read_object.schema
	deleted:    api/request_definitions/templates/POST_validate_payload_against_schema.schema
	deleted:    api/scripts/__init__.py
	deleted:    api/scripts/method_specific/GET_draft_object_by_id.py
	deleted:    api/scripts/method_specific/GET_published_object_by_id.py
	deleted:    api/scripts/method_specific/GET_published_object_by_id_with_version.py
	deleted:    api/scripts/method_specific/GET_retrieve_available_schema.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_create.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_delete.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_modify.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_permissions.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_permissions_set.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_publish.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_read.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_token.py
	deleted:    api/scripts/method_specific/POST_api_objects_publish.py
	deleted:    api/scripts/method_specific/POST_api_objects_published.py
	deleted:    api/scripts/method_specific/POST_api_objects_search.py
	deleted:    api/scripts/method_specific/POST_api_objects_token.py
	deleted:    api/scripts/method_specific/POST_validate_payload_against_schema.py
	deleted:    api/scripts/method_specific/__init__.py
	deleted:    api/scripts/utilities/DbUtils.py
	deleted:    api/scripts/utilities/FileUtils.py
	deleted:    api/scripts/utilities/JsonUtils.py
	deleted:    api/scripts/utilities/RequestUtils.py
	deleted:    api/scripts/utilities/ResponseUtils.py
	deleted:    api/scripts/utilities/SettingsUtils.py
	deleted:    api/scripts/utilities/UserUtils.py
	deleted:    api/scripts/utilities/__init__.py
	deleted:    api/serializers.py
	deleted:    api/signals.py
	deleted:    api/templates/api/account_activation_message.html
	deleted:    api/urls.py
	deleted:    api/validation_definitions/IEEE/2791object.json
	deleted:    api/validation_definitions/IEEE/description_domain.json
	deleted:    api/validation_definitions/IEEE/error_domain.json
	deleted:    api/validation_definitions/IEEE/execution_domain.json
	deleted:    api/validation_definitions/IEEE/io_domain.json
	deleted:    api/validation_definitions/IEEE/parametric_domain.json
	deleted:    api/validation_definitions/IEEE/provenance_domain.json
	deleted:    api/validation_definitions/IEEE/usability_domain.json
	deleted:    api/validation_definitions/IEEE_sub/IEEE2791-2020.schema
	deleted:    api/validation_definitions/IEEE_sub/domains/description_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/error_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/execution_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/io_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/parametric_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/provenance_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/usability_domain.json
	deleted:    api/validation_definitions/uri_external
	deleted:    api/views.py
	new file:   config/settings.py
	modified:   config/urls.py

Changes not staged for commit:
	modified:   authentication/apis.py
	modified:   authentication/migrations/0001_initial.py
	deleted:    authentication/migrations/0002_newuser.py
	modified:   authentication/services.py
	modified:   docs/refactor.md
	modified:   search/selectors.py
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_database.py
	deleted:    tests/test_fixtures.py
	deleted:    tests/test_models
	modified:   tests/test_views/test_api_account_activate.py
	deleted:    tests/test_views/test_api_accounts_describe.py
	modified:   tests/test_views/test_api_auth_add.py
	modified:   tests/test_views/test_api_auth_reset_token.py
	deleted:    tests/test_views/test_api_groups_group_info.py
	deleted:    tests/test_views/test_api_groups_modify.py
	deleted:    tests/test_views/test_api_objects.py
	deleted:    tests/test_views/test_api_objects_drafts_create.py
	deleted:    tests/test_views/test_api_objects_drafts_modify.py
	deleted:    tests/test_views/test_api_objects_drafts_publish.py
	deleted:    tests/test_views/test_api_objects_search.py
	deleted:    tests/test_views/test_api_objects_validate.py
	deleted:    tests/test_views/test_api_prefixes_create.py
	deleted:    tests/test_views/test_api_prefixes_token.py
	deleted:    tests/test_views/test_get_object_id_draft.py
	deleted:    tests/test_views/test_get_objectid.py
	deleted:    tests/test_views/test_published_object_by_id.py
	modified:   token.json

* Framework for BioCompute model

Changes to be committed:
	new file:   biocompute/__init__.py
	new file:   biocompute/admin.py
	new file:   biocompute/apis.py
	new file:   biocompute/migrations/__init__.py
	new file:   biocompute/models.py
	new file:   biocompute/selectors.py
	new file:   biocompute/services.py
	new file:   biocompute/urls.py

* Added files for Prefix model

Changes to be committed:
	new file:   prefix/__init__.py
	new file:   prefix/admin.py
	new file:   prefix/apis.py
	new file:   prefix/apps.py
	new file:   prefix/migrations/__init__.py
	new file:   prefix/models.py
	new file:   prefix/selectors.py
	new file:   prefix/services.py
	new file:   prefix/urls.py

* Tests for authentication

Changes to be committed:
	modified:   .gitignore
	modified:   authentication/apis.py
	modified:   authentication/migrations/0001_initial.py
	deleted:    authentication/migrations/0002_newuser.py
	modified:   authentication/services.py
	new file:   biocompute/migrations/0001_initial.py
	modified:   docs/refactor.md
	new file:   prefix/migrations/0001_initial.py
	modified:   search/selectors.py
	new file:   test.json
	new file:   tests/fixtures/old_test_data.json
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_database.py
	deleted:    tests/test_fixtures.py
	deleted:    tests/test_models
	modified:   tests/test_views/test_api_account_activate.py
	renamed:    tests/test_views/test_api_accounts_describe.py -> tests/test_views/test_api_account_describe.py
	modified:   tests/test_views/test_api_auth_add.py
	modified:   tests/test_views/test_api_auth_reset_token.py
	deleted:    tests/test_views/test_api_groups_group_info.py
	deleted:    tests/test_views/test_api_groups_modify.py
	deleted:    tests/test_views/test_api_objects.py
	deleted:    tests/test_views/test_api_objects_drafts_create.py
	deleted:    tests/test_views/test_api_objects_drafts_modify.py
	deleted:    tests/test_views/test_api_objects_drafts_publish.py
	deleted:    tests/test_views/test_api_objects_search.py
	deleted:    tests/test_views/test_api_objects_validate.py
	deleted:    tests/test_views/test_api_prefixes_create.py
	deleted:    tests/test_views/test_api_prefixes_token.py
	deleted:    tests/test_views/test_get_object_id_draft.py
	deleted:    tests/test_views/test_get_objectid.py
	deleted:    tests/test_views/test_published_object_by_id.py
	modified:   token.json

* Move Swagger files and implement BCO draft create

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	new file:   config/services.py
	modified:   config/urls.py
	modified:   docs/refactor.md
	modified:   prefix/urls.py
	new file:   tests/fixtures/example_bco.py
	new file:   tests/test_views/test_api_objects_drafts_create.py

* Doc fix in Bco.models
Changes to be committed:
	modified:   biocompute/models.py

* Biocompute model (#284)

* Remove API app
Changes to be committed:
	deleted:    api/__init__.py
	deleted:    api/admin.py
	deleted:    api/apps.py
	deleted:    api/fixtures/bootstrap.json
	deleted:    api/fixtures/metafixtures
	deleted:    api/fixtures/metafixtures.json
	deleted:    api/keys.sh
	deleted:    api/migrations/0001_initial.py
	deleted:    api/migrations/0002_auto_20220124_2356.py
	deleted:    api/migrations/0003_rename_meta_table_prefix_table.py
	deleted:    api/migrations/0004_rename_group_info_groupinfo.py
	deleted:    api/migrations/0005_rename_prefixes_prefix.py
	deleted:    api/migrations/0006_delete_new_users.py
	deleted:    api/migrations/__init__.py
	deleted:    api/model/__init__.py
	deleted:    api/model/groups.py
	deleted:    api/model/prefix.py
	deleted:    api/models.py
	deleted:    api/permissions.py
	deleted:    api/rdb.sh
	deleted:    api/request_definitions/GET.schema
	deleted:    api/request_definitions/POST.schema
	deleted:    api/request_definitions/templates/DELETE_delete_object_by_id.schema
	deleted:    api/request_definitions/templates/GET_activate_account.schema
	deleted:    api/request_definitions/templates/GET_get_object_by_id.schema
	deleted:    api/request_definitions/templates/GET_retrieve_available_schema.schema
	deleted:    api/request_definitions/templates/POST_convert_existing_object_between_schemas.schema
	deleted:    api/request_definitions/templates/POST_convert_payload_to_schema.schema
	deleted:    api/request_definitions/templates/POST_new_account.schema
	deleted:    api/request_definitions/templates/POST_object_listing_by_token.schema
	deleted:    api/request_definitions/templates/POST_objects_draft.schema
	deleted:    api/request_definitions/templates/POST_objects_publish.schema
	deleted:    api/request_definitions/templates/POST_read_object.schema
	deleted:    api/request_definitions/templates/POST_validate_payload_against_schema.schema
	deleted:    api/scripts/__init__.py
	deleted:    api/scripts/method_specific/GET_draft_object_by_id.py
	deleted:    api/scripts/method_specific/GET_published_object_by_id.py
	deleted:    api/scripts/method_specific/GET_published_object_by_id_with_version.py
	deleted:    api/scripts/method_specific/GET_retrieve_available_schema.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_create.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_delete.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_modify.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_permissions.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_permissions_set.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_publish.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_read.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_token.py
	deleted:    api/scripts/method_specific/POST_api_objects_publish.py
	deleted:    api/scripts/method_specific/POST_api_objects_published.py
	deleted:    api/scripts/method_specific/POST_api_objects_search.py
	deleted:    api/scripts/method_specific/POST_api_objects_token.py
	deleted:    api/scripts/method_specific/POST_validate_payload_against_schema.py
	deleted:    api/scripts/method_specific/__init__.py
	deleted:    api/scripts/utilities/DbUtils.py
	deleted:    api/scripts/utilities/FileUtils.py
	deleted:    api/scripts/utilities/JsonUtils.py
	deleted:    api/scripts/utilities/RequestUtils.py
	deleted:    api/scripts/utilities/ResponseUtils.py
	deleted:    api/scripts/utilities/SettingsUtils.py
	deleted:    api/scripts/utilities/UserUtils.py
	deleted:    api/scripts/utilities/__init__.py
	deleted:    api/serializers.py
	deleted:    api/signals.py
	deleted:    api/templates/api/account_activation_message.html
	deleted:    api/urls.py
	deleted:    api/validation_definitions/IEEE/2791object.json
	deleted:    api/validation_definitions/IEEE/description_domain.json
	deleted:    api/validation_definitions/IEEE/error_domain.json
	deleted:    api/validation_definitions/IEEE/execution_domain.json
	deleted:    api/validation_definitions/IEEE/io_domain.json
	deleted:    api/validation_definitions/IEEE/parametric_domain.json
	deleted:    api/validation_definitions/IEEE/provenance_domain.json
	deleted:    api/validation_definitions/IEEE/usability_domain.json
	deleted:    api/validation_definitions/IEEE_sub/IEEE2791-2020.schema
	deleted:    api/validation_definitions/IEEE_sub/domains/description_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/error_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/execution_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/io_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/parametric_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/provenance_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/usability_domain.json
	deleted:    api/validation_definitions/uri_external
	deleted:    api/views.py
	new file:   config/settings.py
	modified:   config/urls.py

Changes not staged for commit:
	modified:   authentication/apis.py
	modified:   authentication/migrations/0001_initial.py
	deleted:    authentication/migrations/0002_newuser.py
	modified:   authentication/services.py
	modified:   docs/refactor.md
	modified:   search/selectors.py
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_database.py
	deleted:    tests/test_fixtures.py
	deleted:    tests/test_models
	modified:   tests/test_views/test_api_account_activate.py
	deleted:    tests/test_views/test_api_accounts_describe.py
	modified:   tests/test_views/test_api_auth_add.py
	modified:   tests/test_views/test_api_auth_reset_token.py
	deleted:    tests/test_views/test_api_groups_group_info.py
	deleted:    tests/test_views/test_api_groups_modify.py
	deleted:    tests/test_views/test_api_objects.py
	deleted:    tests/test_views/test_api_objects_drafts_create.py
	deleted:    tests/test_views/test_api_objects_drafts_modify.py
	deleted:    tests/test_views/test_api_objects_drafts_publish.py
	deleted:    tests/test_views/test_api_objects_search.py
	deleted:    tests/test_views/test_api_objects_validate.py
	deleted:    tests/test_views/test_api_prefixes_create.py
	deleted:    tests/test_views/test_api_prefixes_token.py
	deleted:    tests/test_views/test_get_object_id_draft.py
	deleted:    tests/test_views/test_get_objectid.py
	deleted:    tests/test_views/test_published_object_by_id.py
	modified:   token.json

* Framework for BioCompute model

Changes to be committed:
	new file:   biocompute/__init__.py
	new file:   biocompute/admin.py
	new file:   biocompute/apis.py
	new file:   biocompute/migrations/__init__.py
	new file:   biocompute/models.py
	new file:   biocompute/selectors.py
	new file:   biocompute/services.py
	new file:   biocompute/urls.py

* Added files for Prefix model

Changes to be committed:
	new file:   prefix/__init__.py
	new file:   prefix/admin.py
	new file:   prefix/apis.py
	new file:   prefix/apps.py
	new file:   prefix/migrations/__init__.py
	new file:   prefix/models.py
	new file:   prefix/selectors.py
	new file:   prefix/services.py
	new file:   prefix/urls.py

* Tests for authentication

Changes to be committed:
	modified:   .gitignore
	modified:   authentication/apis.py
	modified:   authentication/migrations/0001_initial.py
	deleted:    authentication/migrations/0002_newuser.py
	modified:   authentication/services.py
	new file:   biocompute/migrations/0001_initial.py
	modified:   docs/refactor.md
	new file:   prefix/migrations/0001_initial.py
	modified:   search/selectors.py
	new file:   test.json
	new file:   tests/fixtures/old_test_data.json
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_database.py
	deleted:    tests/test_fixtures.py
	deleted:    tests/test_models
	modified:   tests/test_views/test_api_account_activate.py
	renamed:    tests/test_views/test_api_accounts_describe.py -> tests/test_views/test_api_account_describe.py
	modified:   tests/test_views/test_api_auth_add.py
	modified:   tests/test_views/test_api_auth_reset_token.py
	deleted:    tests/test_views/test_api_groups_group_info.py
	deleted:    tests/test_views/test_api_groups_modify.py
	deleted:    tests/test_views/test_api_objects.py
	deleted:    tests/test_views/test_api_objects_drafts_create.py
	deleted:    tests/test_views/test_api_objects_drafts_modify.py
	deleted:    tests/test_views/test_api_objects_drafts_publish.py
	deleted:    tests/test_views/test_api_objects_search.py
	deleted:    tests/test_views/test_api_objects_validate.py
	deleted:    tests/test_views/test_api_prefixes_create.py
	deleted:    tests/test_views/test_api_prefixes_token.py
	deleted:    tests/test_views/test_get_object_id_draft.py
	deleted:    tests/test_views/test_get_objectid.py
	deleted:    tests/test_views/test_published_object_by_id.py
	modified:   token.json

* Move Swagger files and implement BCO draft create

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	new file:   config/services.py
	modified:   config/urls.py
	modified:   docs/refactor.md
	modified:   prefix/urls.py
	new file:   tests/fixtures/example_bco.py
	new file:   tests/test_views/test_api_objects_drafts_create.py

* Doc fix in Bco.models
Changes to be committed:
	modified:   biocompute/models.py

* Updated biocompute.model and prefix.model

Added the DraftsCreateApi and tests.
This included serializers for BCO creation
Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/services.py
	modified:   config/services.py
	modified:   prefix/models.py
	modified:   prefix/services.py
	modified:   test.json
	modified:   tests/fixtures/test_data.json
	new file:   tests/test_views/test_api_objects_drafts_create.py

* Implemented PrefixesCreateApi

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   config/fixtures/local_data.json
	modified:   config/services.py
	modified:   config/urls.py
	modified:   prefix/apis.py
	modified:   prefix/services.py
	modified:   prefix/urls.py
	modified:   search/apis.py
	modified:   tests/test_views/test_api_auth_remove.py
	modified:   tests/test_views/test_api_objects_drafts_create.py
	new file:   tests/test_views/test_api_prefixes_create.py

* Added Prefix management URLs and APIs

Changes to be committed:
	modified:   config/fixtures/local_data.json
	modified:   docs/refactor.md
	modified:   prefix/apis.py
	modified:   prefix/services.py
	modified:   prefix/urls.py
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_views/test_api_prefixes_create.py
	new file:   tests/test_views/test_prefixes_create.py
	new file:   tests/test_views/test_prefixes_modify.py

* Cleaning up some things
Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/migrations/0001_initial.py
	modified:   prefix/apis.py
	modified:   prefix/migrations/0001_initial.py
	new file:   tests/test_views/test_account_activate.py
	new file:   tests/test_views/test_account_describe.py
	new file:   tests/test_views/test_account_new.py
	new file:   tests/test_views/test_auth_add.py
	new file:   tests/test_views/test_auth_remove.py
	new file:   tests/test_views/test_auth_reset_token.py
	new file:   tests/test_views/test_objects_drafts_create.py

* Add prefix creation function
Changes to be committed:
	modified:   authentication/services.py
	modified:   biocompute/models.py
	modified:   config/settings.py
	modified:   docs/refactor.md
	modified:   prefix/apis.py
	modified:   prefix/models.py
	modified:   prefix/services.py
	modified:   tests/test_views/test_api_objects_drafts_create.py

* Add Prefix Modify API endpoint
On branch prefix_perms
Your branch is up to date with 'origin/prefix_perms'.

Changes to be committed:
	modified:   config/services.py
	modified:   prefix/apis.py
	modified:   prefix/models.py
	modified:   prefix/selectors.py
	modified:   prefix/services.py

* response_c

* Add `DraftRetrieveApi`

To do this functions related to Prefixes and the associated permissions were created

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   biocompute/selectors.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	modified:   config/asgi.py
	modified:   config/fixtures/local_data.json
	modified:   config/services.py
	modified:   config/urls.py
	modified:   prefix/selectors.py
	modified:   prefix/services.py
	deleted:    test.json
	modified:   tests/fixtures/example_bco.py
	modified:   tests/fixtures/test_data.json
	deleted:    token.json

* Update testing functions

Created subdirectory and moved test functions
Changes to be committed:
	renamed:    tests/test_views/__init__.py -> tests/test_apis/__init__.py
	new file:   tests/test_apis/test_api_authentication/__init__.py
	renamed:    tests/test_views/test_account_activate.py -> tests/test_apis/test_api_authentication/test_account_activate.py
	renamed:    tests/test_views/test_account_describe.py -> tests/test_apis/test_api_authentication/test_account_describe.py
	renamed:    tests/test_views/test_account_new.py -> tests/test_apis/test_api_authentication/test_account_new.py
	renamed:    tests/test_views/test_api_auth_add.py -> tests/test_apis/test_api_authentication/test_api_auth_add.py
	renamed:    tests/test_views/test_api_auth_remove.py -> tests/test_apis/test_api_authentication/test_api_auth_remove.py
	renamed:    tests/test_views/test_api_auth_reset_token.py -> tests/test_apis/test_api_authentication/test_api_auth_reset_token.py
	renamed:    tests/test_views/test_api_objects_drafts_create.py -> tests/test_apis/test_api_objects_drafts_create.py
	renamed:    tests/test_views/test_auth_add.py -> tests/test_apis/test_auth_add.py
	renamed:    tests/test_views/test_auth_remove.py -> tests/test_apis/test_auth_remove.py
	renamed:    tests/test_views/test_auth_reset_token.py -> tests/test_apis/test_auth_reset_token.py
	renamed:    tests/test_views/test_objects_drafts_create.py -> tests/test_apis/test_objects_drafts_create.py
	renamed:    tests/test_views/test_prefixes_create.py -> tests/test_apis/test_prefixes_create.py
	new file:   tests/test_apis/test_prefixes_modify.py
	deleted:    tests/test_views/test_api_account_activate.py
	deleted:    tests/test_views/test_api_account_describe.py
	deleted:    tests/test_views/test_api_account_new.py
	deleted:    tests/test_views/test_prefixes_modify.py

* Add `DraftRetrieveApi`

To do this functions related to Prefixes and the associated permissions were created

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   biocompute/selectors.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	modified:   config/asgi.py
	modified:   config/fixtures/local_data.json
	modified:   config/services.py
	modified:   config/urls.py
	modified:   prefix/selectors.py
	modified:   prefix/services.py
	deleted:    test.json
	modified:   tests/fixtures/example_bco.py
	modified:   tests/fixtures/test_data.json
	deleted:    token.json

* Update testing functions

Created subdirectory and moved test functions
Changes to be committed:
	renamed:    tests/test_views/__init__.py -> tests/test_apis/__init__.py
	new file:   tests/test_apis/test_api_authentication/__init__.py
	renamed:    tests/test_views/test_account_activate.py -> tests/test_apis/test_api_authentication/test_account_activate.py
	renamed:    tests/test_views/test_account_describe.py -> tests/test_apis/test_api_authentication/test_account_describe.py
	renamed:    tests/test_views/test_account_new.py -> tests/test_apis/test_api_authentication/test_account_new.py
	renamed:    tests/test_views/test_api_auth_add.py -> tests/test_apis/test_api_authentication/test_api_auth_add.py
	renamed:    tests/test_views/test_api_auth_remove.py -> tests/test_apis/test_api_authentication/test_api_auth_remove.py
	renamed:    tests/test_views/test_api_auth_reset_token.py -> tests/test_apis/test_api_authentication/test_api_auth_reset_token.py
	renamed:    tests/test_views/test_api_objects_drafts_create.py -> tests/test_apis/test_api_objects_drafts_create.py
	renamed:    tests/test_views/test_auth_add.py -> tests/test_apis/test_auth_add.py
	renamed:    tests/test_views/test_auth_remove.py -> tests/test_apis/test_auth_remove.py
	renamed:    tests/test_views/test_auth_reset_token.py -> tests/test_apis/test_auth_reset_token.py
	renamed:    tests/test_views/test_objects_drafts_create.py -> tests/test_apis/test_objects_drafts_create.py
	renamed:    tests/test_views/test_prefixes_create.py -> tests/test_apis/test_prefixes_create.py
	new file:   tests/test_apis/test_prefixes_modify.py
	deleted:    tests/test_views/test_api_account_activate.py
	deleted:    tests/test_views/test_api_account_describe.py
	deleted:    tests/test_views/test_api_account_new.py
	deleted:    tests/test_views/test_prefixes_modify.py

* Update to Test functions

Changes to be committed:
	modified:   biocompute/migrations/0001_initial.py
	modified:   docs/refactor.md
	modified:   prefix/apis.py
	modified:   prefix/migrations/0001_initial.py
	modified:   prefix/services.py
	new file:   tests/fixtures/bco_dump.json
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_apis/test_api_authentication/test_api_auth_add.py
	deleted:    tests/test_apis/test_api_authentication/test_api_auth_reset_token.py
	renamed:    tests/test_apis/test_auth_add.py -> tests/test_apis/test_api_authentication/test_auth_add.py
	renamed:    tests/test_apis/test_auth_reset_token.py -> tests/test_apis/test_api_authentication/test_auth_reset_token.py
	renamed:    tests/test_apis/test_api_authentication/test_api_auth_remove.py -> tests/test_apis/test_api_authentication/testi_auth_remove.py
	deleted:    tests/test_apis/test_api_objects_drafts_create.py
	new file:   tests/test_apis/test_api_prefix/__init__.py
	renamed:    tests/test_apis/test_prefixes_create.py -> tests/test_apis/test_api_prefix/test_prefixes_create.py
	renamed:    tests/test_apis/test_prefixes_modify.py -> tests/test_apis/test_api_prefix/test_prefixes_modify.py
	deleted:    tests/test_apis/test_auth_remove.py
	new file:   tests/test_apis/test_biocompute/__init__.py
	renamed:    tests/test_apis/test_objects_drafts_create.py -> tests/test_apis/test_biocompute/test_objects_drafts_create.py

* Bco perms (#293)

* Add `DraftRetrieveApi`

To do this functions related to Prefixes and the associated permissions were created

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   biocompute/selectors.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	modified:   config/asgi.py
	modified:   config/fixtures/local_data.json
	modified:   config/services.py
	modified:   config/urls.py
	modified:   prefix/selectors.py
	modified:   prefix/services.py
	deleted:    test.json
	modified:   tests/fixtures/example_bco.py
	modified:   tests/fixtures/test_data.json
	deleted:    token.json

* Update testing functions

Created subdirectory and moved test functions
Changes to be committed:
	renamed:    tests/test_views/__init__.py -> tests/test_apis/__init__.py
	new file:   tests/test_apis/test_api_authentication/__init__.py
	renamed:    tests/test_views/test_account_activate.py -> tests/test_apis/test_api_authentication/test_account_activate.py
	renamed:    tests/test_views/test_account_describe.py -> tests/test_apis/test_api_authentication/test_account_describe.py
	renamed:    tests/test_views/test_account_new.py -> tests/test_apis/test_api_authentication/test_account_new.py
	renamed:    tests/test_views/test_api_auth_add.py -> tests/test_apis/test_api_authentication/test_api_auth_add.py
	renamed:    tests/test_views/test_api_auth_remove.py -> tests/test_apis/test_api_authentication/test_api_auth_remove.py
	renamed:    tests/test_views/test_api_auth_reset_token.py -> tests/test_apis/test_api_authentication/test_api_auth_reset_token.py
	renamed:    tests/test_views/test_api_objects_drafts_create.py -> tests/test_apis/test_api_objects_drafts_create.py
	renamed:    tests/test_views/test_auth_add.py -> tests/test_apis/test_auth_add.py
	renamed:    tests/test_views/test_auth_remove.py -> tests/test_apis/test_auth_remove.py
	renamed:    tests/test_views/test_auth_reset_token.py -> tests/test_apis/test_auth_reset_token.py
	renamed:    tests/test_views/test_objects_drafts_create.py -> tests/test_apis/test_objects_drafts_create.py
	renamed:    tests/test_views/test_prefixes_create.py -> tests/test_apis/test_prefixes_create.py
	new file:   tests/test_apis/test_prefixes_modify.py
	deleted:    tests/test_views/test_api_account_activate.py
	deleted:    tests/test_views/test_api_account_describe.py
	deleted:    tests/test_views/test_api_account_new.py
	deleted:    tests/test_views/test_prefixes_modify.py

* Update to Test functions

Changes to be committed:
	modified:   biocompute/migrations/0001_initial.py
	modified:   docs/refactor.md
	modified:   prefix/apis.py
	modified:   prefix/migrations/0001_initial.py
	modified:   prefix/services.py
	new file:   tests/fixtures/bco_dump.json
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_apis/test_api_authentication/test_api_auth_add.py
	deleted:    tests/test_apis/test_api_authentication/test_api_auth_reset_token.py
	renamed:    tests/test_apis/test_auth_add.py -> tests/test_apis/test_api_authentication/test_auth_add.py
	renamed:    tests/test_apis/test_auth_reset_token.py -> tests/test_apis/test_api_authentication/test_auth_reset_token.py
	renamed:    tests/test_apis/test_api_authentication/test_api_auth_remove.py -> tests/test_apis/test_api_authentication/testi_auth_remove.py
	deleted:    tests/test_apis/test_api_objects_drafts_create.py
	new file:   tests/test_apis/test_api_prefix/__init__.py
	renamed:    tests/test_apis/test_prefixes_create.py -> tests/test_apis/test_api_prefix/test_prefixes_create.py
	renamed:    tests/test_apis/test_prefixes_modify.py -> tests/test_apis/test_api_prefix/test_prefixes_modify.py
	deleted:    tests/test_apis/test_auth_remove.py
	new file:   tests/test_apis/test_biocompute/__init__.py
	renamed:    tests/test_apis/test_objects_drafts_create.py -> tests/test_apis/test_biocompute/test_objects_drafts_create.py

* Add `access_count` incrementer to DraftRetrieveApi

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/services.py
	modified:   prefix/services.py

* Added PublishedRetrieveApi class
Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/selectors.py
	modified:   config/urls.py

* Update test DB and testing functions

Changes to be committed:
	modified:   config/fixtures/local_data.json
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_apis/test_api_objects_drafts_create.py
	deleted:    tests/test_apis/test_auth_add.py
	deleted:    tests/test_apis/test_auth_remove.py
	deleted:    tests/test_apis/test_auth_reset_token.py
	renamed:    tests/test_apis/test_objects_drafts_create.py -> tests/test_apis/test_biocompute/objects_drafts_create.py
	deleted:    tests/test_apis/test_prefixes_create.py
	deleted:    tests/test_apis/test_prefixes_modify.py

* Add DraftsModifyApi

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/selectors.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	modified:   prefix/selectors.py
	deleted:    tests/test_apis/test_biocompute/objects_drafts_create.py
	deleted:    tests/test_apis/test_biocompute/test_objects_drafts_create.py

* test for objects_drafts_create

Changes to be committed:
	new file:   tests/test_apis/test_biocompute/test_objects_drafts_create.py

* split("/")

* Publish draft (#308)

* Add DraftsModifyApi

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/selectors.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	modified:   prefix/selectors.py
	deleted:    tests/test_apis/test_biocompute/objects_drafts_create.py
	deleted:    tests/test_apis/test_biocompute/test_objects_drafts_create.py

* Add IEEE schema
Changes to be committed:
	new file:   .secrets
	new file:   config/IEEE/2791object.json
	new file:   config/IEEE/description_domain.json
	new file:   config/IEEE/error_domain.json
	new file:   config/IEEE/execution_domain.json
	new file:   config/IEEE/io_domain.json
	new file:   config/IEEE/parametric_domain.json
	new file:   config/IEEE/provenance_domain.json
	new file:   config/IEEE/usability_domain.json

* test_objects_drafts_create
Changes to be committed:
	new file:   tests/test_apis/test_biocompute/test_objects_drafts_create.py

* Fix test
Changes to be committed:
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_create.py

* Enable publish bco endpoint

This included a great many supporting functions
and permission checks to accomplish. Also added
the validate functions to the codebase

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/selectors.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	modified:   config/services.py
	modified:   docs/refactor.md
	modified:   prefix/selectors.py
	new file:   tests/test_apis/test_biocompute/test_objects_drafts_publish.py

* Add BCO Score to model.

Also added functions and methods for BCO Score.
Updates to the BCO admin panel.
Updates to the `test_data.json` and `local_data.json`
Fix # 310
Changes to be committed:
	modified:   authentication/migrations/0001_initial.py
	modified:   biocompute/admin.py
	modified:   biocompute/apis.py
	modified:   biocompute/migrations/0001_initial.py
	modified:   biocompute/models.py
	modified:   biocompute/services.py
	new file:   config/bco_scores.py
	modified:   config/fixtures/local_data.json
	modified:   tests/fixtures/test_data.json

* Add BCODB search API endpoint.

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   search/apis.py
	modified:   search/selectors.py
	modified:   search/urls.py

* Add POST search
Changes to be committed:
	modified:   authentication/apis.py
	modified:   search/apis.py

* Updated config file to `.secrets`

also updated accounts/describe
Changes to be committed:
	modified:   .gitignore
	new file:   .secrets.example
	modified:   authentication/selectors.py
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   biocompute/selectors.py
	modified:   config/settings.py
	deleted:    server.conf
	deleted:    sever.conf.example

* Fix config/urls.py error
Changes to be committed:
	deleted:    .secrets
	modified:   config/settings.py
	modified:   config/urls.py

* Refactor `config/services.py::response_constructor`
Changes to be committed:
	modified:   config/services.py
	modified:   tests/test_apis/test_api_prefix/test_prefixes_create.py

* Prefix registry (#318)

* Created test_objects_drafts_modify, hasn't passed test yet

* Created test_objects_drafts_modify, hasn't passed test yet

* Created test_objects_drafts_modify, hasn't passed test yet

* new tests

* Update modify_prefix permissions
Changes to be committed:
	modified:   authentication/selectors.py
	modified:   config/fixtures/local_data.json
	modified:   prefix/services.py

* Created and tested test_objects_drafts_modify API

* Fixes for Prefix creation

Changes to be committed:
	modified:   config/services.py
	modified:   prefix/apis.py
	modified:   tests/test_apis/test_api_prefix/test_prefixes_create.py

* Add UserSearch endpoint

Changes to be committed:
	modified:   prefix/apis.py
	modified:   prefix/selectors.py
	modified:   search/apis.py
	modified:   search/urls.py

* Fixes for deployment

 Changes to be committed:
	modified:   .secrets.example
	modified:   admin_only/bco_api.service
	modified:   biocompute/apis.py
	modified:   config/fixtures/test_portal.json
	modified:   config/settings.py
	modified:   tests/fixtures/test_data.json
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_create.py

* test_objects_drafts_publish failed. Kicking back to Hadley for more investigation

* Update bco_api.conf

Changes to be committed:
	modified:   admin_only/bco_api.conf

---------

Co-authored-by: tianywan819 <[email protected]>
Co-authored-by: acoleman29 <[email protected]>

* Fixes for testing files

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/services.py
	modified:   config/bco_scores.py
	modified:   config/services.py
	modified:   config/settings.py
	modified:   config/urls.py
	modified:   tests/fixtures/test_data.json
	renamed:    tests/fixtures/example_bco.py -> tests/fixtures/testing_bcos.py
	modified:   tests/test_apis/test_api_prefix/test_prefixes_create.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_modify.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_publish.py

* "derrived_from": []

* fix test

* Add Validate url endpoint

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/urls.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_create.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_publish.py

* Update create test to include HOSTNAME

Changes to be committed:
	modified:   config/services.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_create.py

* Rollback status for validation

Changes to be committed:
	modified:   biocompute/apis.py

* Changes to be committed:
	modified:   biocompute/apis.py

* Typo fix
Changes to be committed:
	modified:   biocompute/apis.py

* Add `test_portal.json` for testing

Changes to be committed:
	modified:   config/fixtures/test_portal.json

* Testing fixes

Changes to be committed:
	modified:   admin_only/bco_api.conf
	modified:   config/fixtures/test_portal.json

* Fix for draft publish

Changes to be committed:
	modified:   config/services.py

* Add new_bco_instance.save()

Changes to be committed:
	modified:   biocompute/services.py
	modified:   config/services.py

* CustomJSONWebTokenAuthentication for GET Pub BCO
Changes to be committed:
	modified:   biocompute/apis.py

* Updates to authentication.apis.py
Changes to be committed:
	modified:   authentication/apis.py
	modified:   authentication/services.py
	modified:   search/apis.py

* Updates to biocompute.apis.py

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/selectors.py
	modified:   search/apis.py
	modified:   tests/fixtures/testing_bcos.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_create.py

* Remove print statements

Changes to be committed:
	modified:   authentication/apis.py
	modified:   authentication/services.py
	modified:   authentication/urls.py
	modified:   biocompute/apis.py
	modified:   biocompute/services.py
	modified:   config/urls.py
	modified:   prefix/services.py
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_publish.py

* Updates to prefix.apis

Changes to be committed:
	modified:   prefix/apis.py

* print(

* change publish bco rejected response

On branch docs
Your branch is up to date with 'origin/docs'.

---------

Co-authored-by: tianywan819 <[email protected]>
Co-authored-by: acoleman29 <[email protected]>
@HadleyKing HadleyKing mentioned this pull request May 20, 2024
Closed
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@HadleyKing