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Dev #345

Merged
merged 10 commits into from
Aug 22, 2024
Merged

Dev #345

merged 10 commits into from
Aug 22, 2024

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HadleyKing
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Kirans0615 and others added 9 commits July 22, 2024 17:31
Changes to be committed:
	deleted:    docs/bco_scores.json
	modified:   docs/deployment/productionDeployment.md
	new file:   docs/newProductionInstance.md
Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/urls.py
	modified:   requirements.txt
biocompute-objects/portal_userdb#380

Changes to be committed:
	modified:   .github/workflows/django.yml
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   config/settings.py
	modified:   config/urls.py
Updated the function to check locally for the most used schemas. Improves
testing and speed in BCO validation.

Changes to be committed:
	modified:   biocompute/services.py
	renamed:    config/IEEE/2791object.json -> config/schemas/2791object.json
	new file:   config/schemas/dataset_extension.json
	renamed:    config/IEEE/description_domain.json -> config/schemas/description_domain.json
	renamed:    config/IEEE/error_domain.json -> config/schemas/error_domain.json
	renamed:    config/IEEE/execution_domain.json -> config/schemas/execution_domain.json
	new file:   config/schemas/fhir_extension.json
	new file:   config/schemas/galaxy_extension.json
	renamed:    config/IEEE/io_domain.json -> config/schemas/io_domain.json
	new file:   config/schemas/license_extension.json
	renamed:    config/IEEE/parametric_domain.json -> config/schemas/parametric_domain.json
	renamed:    config/IEEE/provenance_domain.json -> config/schemas/provenance_domain.json
	new file:   config/schemas/scm_extension.json
	renamed:    config/IEEE/usability_domain.json -> config/schemas/usability_domain.json
Changes to be committed:
	modified:   biocompute/services.py
	new file:   config/schemas/1.1.0/dataset_extension.json
	new file:   config/schemas/1.1.0/fhir_extension.json
	new file:   config/schemas/1.1.0/galaxy_extension.json
	new file:   config/schemas/1.1.0/license_extension.json
	new file:   config/schemas/1.1.0/scm_extension.json
	renamed:    config/schemas/dataset_extension.json -> config/schemas/1.2.0/dataset_extension.json
	renamed:    config/schemas/fhir_extension.json -> config/schemas/1.2.0/fhir_extension.json
	renamed:    config/schemas/galaxy_extension.json -> config/schemas/1.2.0/galaxy_extension.json
	renamed:    config/schemas/license_extension.json -> config/schemas/1.2.0/license_extension.json
	renamed:    config/schemas/scm_extension.json -> config/schemas/1.2.0/scm_extension.json
	renamed:    config/schemas/2791object.json -> config/schemas/2791/2791object.json
	renamed:    config/schemas/description_domain.json -> config/schemas/2791/description_domain.json
	renamed:    config/schemas/error_domain.json -> config/schemas/2791/error_domain.json
	renamed:    config/schemas/execution_domain.json -> config/schemas/2791/execution_domain.json
	renamed:    config/schemas/io_domain.json -> config/schemas/2791/io_domain.json
	renamed:    config/schemas/parametric_domain.json -> config/schemas/2791/parametric_domain.json
	renamed:    config/schemas/provenance_domain.json -> config/schemas/2791/provenance_domain.json
	renamed:    config/schemas/usability_domain.json -> config/schemas/2791/usability_domain.json
	modified:   config/settings.py
	modified:   requirements.txt
Changes to be committed:
	modified:   Dockerfile
	modified:   docker-compose.yml
	modified:   docs/deployment/dockerDeployment.md
	new file:   entrypoint.sh
Changes to be committed:
	modified:   biocompute/apis.py
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gitguardian bot commented Aug 22, 2024

⚠️ GitGuardian has uncovered 3 secrets following the scan of your pull request.

Please consider investigating the findings and remediating the incidents. Failure to do so may lead to compromising the associated services or software components.

🔎 Detected hardcoded secrets in your pull request
GitGuardian id GitGuardian status Secret Commit Filename
4444553 Triggered Company Email Password efebfbe docker-compose.yml View secret
4444553 Triggered Company Email Password efebfbe Dockerfile View secret
11839907 Triggered Django Secret Key 5c5c1f7 config/settings.py View secret
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@HadleyKing HadleyKing merged commit 40025e8 into 24.08.22 Aug 22, 2024
2 checks passed
HadleyKing added a commit that referenced this pull request Aug 22, 2024
* BCO scoring changes

* Add New Production Deployment md

Changes to be committed:
	deleted:    docs/bco_scores.json
	modified:   docs/deployment/productionDeployment.md
	new file:   docs/newProductionInstance.md

* Update config.md

* Add API endpoint for basic comaprison

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/urls.py
	modified:   requirements.txt

* Fix Django CI issue (#340)

biocompute-objects/portal_userdb#380

Changes to be committed:
	modified:   .github/workflows/django.yml
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   config/settings.py
	modified:   config/urls.py

* Update to BcoValidator.load_schema (#341)

Updated the function to check locally for the most used schemas. Improves
testing and speed in BCO validation.

Changes to be committed:
	modified:   biocompute/services.py
	renamed:    config/IEEE/2791object.json -> config/schemas/2791object.json
	new file:   config/schemas/dataset_extension.json
	renamed:    config/IEEE/description_domain.json -> config/schemas/description_domain.json
	renamed:    config/IEEE/error_domain.json -> config/schemas/error_domain.json
	renamed:    config/IEEE/execution_domain.json -> config/schemas/execution_domain.json
	new file:   config/schemas/fhir_extension.json
	new file:   config/schemas/galaxy_extension.json
	renamed:    config/IEEE/io_domain.json -> config/schemas/io_domain.json
	new file:   config/schemas/license_extension.json
	renamed:    config/IEEE/parametric_domain.json -> config/schemas/parametric_domain.json
	renamed:    config/IEEE/provenance_domain.json -> config/schemas/provenance_domain.json
	new file:   config/schemas/scm_extension.json
	renamed:    config/IEEE/usability_domain.json -> config/schemas/usability_domain.json

* Add additional schema files and reorganize

Changes to be committed:
	modified:   biocompute/services.py
	new file:   config/schemas/1.1.0/dataset_extension.json
	new file:   config/schemas/1.1.0/fhir_extension.json
	new file:   config/schemas/1.1.0/galaxy_extension.json
	new file:   config/schemas/1.1.0/license_extension.json
	new file:   config/schemas/1.1.0/scm_extension.json
	renamed:    config/schemas/dataset_extension.json -> config/schemas/1.2.0/dataset_extension.json
	renamed:    config/schemas/fhir_extension.json -> config/schemas/1.2.0/fhir_extension.json
	renamed:    config/schemas/galaxy_extension.json -> config/schemas/1.2.0/galaxy_extension.json
	renamed:    config/schemas/license_extension.json -> config/schemas/1.2.0/license_extension.json
	renamed:    config/schemas/scm_extension.json -> config/schemas/1.2.0/scm_extension.json
	renamed:    config/schemas/2791object.json -> config/schemas/2791/2791object.json
	renamed:    config/schemas/description_domain.json -> config/schemas/2791/description_domain.json
	renamed:    config/schemas/error_domain.json -> config/schemas/2791/error_domain.json
	renamed:    config/schemas/execution_domain.json -> config/schemas/2791/execution_domain.json
	renamed:    config/schemas/io_domain.json -> config/schemas/2791/io_domain.json
	renamed:    config/schemas/parametric_domain.json -> config/schemas/2791/parametric_domain.json
	renamed:    config/schemas/provenance_domain.json -> config/schemas/2791/provenance_domain.json
	renamed:    config/schemas/usability_domain.json -> config/schemas/2791/usability_domain.json
	modified:   config/settings.py
	modified:   requirements.txt

* Add instructions for Docker deployment

Changes to be committed:
	modified:   Dockerfile
	modified:   docker-compose.yml
	modified:   docs/deployment/dockerDeployment.md
	new file:   entrypoint.sh

* Update comparison API (#344)

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

---------

Co-authored-by: Kiran Sen <[email protected]>
Co-authored-by: Kiran Sen <[email protected]>
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2 participants