Encode-utils

Latest version: v2.11.0

Safety actively analyzes 629599 Python packages for vulnerabilities to keep your Python projects secure.

Scan your dependencies

Page 3 of 5

2.0.0pre

New Features:
1. Added support for transferring ENCODE files to GCP. This comes in a new [[script]](https://encode-utils.readthedocs.io/en/latest/scripts/eu_s3_to_gcp.html) and [[class method]](https://encode-utils.readthedocs.io/en/latest/connection.html#encode_utils.connection.Connection.copy_files_to_gcp) of the Connection class.

Bug Fixes:
1. Fix in Connection class's search() method. Originally, if a query parameter was added twice, i.e. `&status=in+progress&status=submitted`, then only the latter value would be used instead of both. To fix this bug, a backwards incompatible fix was implemented.
1. When uploading files to the Portal, upload_credentials are always first refreshed. It used to be that if they were present, those would be used. The problem was that they may have expired.

1.5.2

Bug fixes:
* Updated ``connection.Connection.regenerate_aws_upload_creds()`` such that it no longer relies on curl and uses the built-in requests module instead. This method simply didn't work for users that didn't have curl installed. It also didn't work for users with slightly older versions of curl installed (special thanks to keenangraham for helping test this out).

* Fixed problem with ``connection.Connection.get_upload_credentials()`` where the credentials weren't present in the downloaded JSON. Fixed this by setting some query parameters in the GET request so that "datastore=database&frame=object" are present in the query segment. This resolves 13.

1.5.1

This release undoes the local schema validation that the previous release introduced.
The schema validation with Python's jsonschema 3rd party library fails when linkTo properties in the schema at hand (i.e. file schema) point to a custom object type (i.e. Platform), since it doesn't understand custom types. So for now, we'll rely on server-side validation in the DCC response, which will soon be providing specific error reasons for schema validation errors.

1.5.0

Added schema validation:
Prior to POSTING, validation is performed on the schema instance (payload) against the profile at hand (i.e. biosample profile). When there is an instance validation error, the details will be printed to STDOUT and logged, and execution will be terminated. The error message gives the exact reason for the validation failure (unlike the DCC server response which might only indicate an invalid instance and not why).

1.4.1

Bug Fix:
Fixes a bug in recent release that prevented user from POSTING objects with eu_register.py as it added a non-schematic profile key by mistake.

Feature update:
``connection.Connection.get()`` now doesn't set a default frame, letting that instead be determined by the ENCODE Portal API, (which sets the default frame to "elasticsearch").

1.4.0

Highlights:
1. New method to download files and documents ``connection.Connection.download()``.
2. Updated ``connection.Connection.search()`` such that the user can now provide a URL with an embedded query string.
3. Updated ``connection.Connection.upload_file()`` such that a new argument is present to allow recalculation of the md5sum and setting that on the file record in the Portal.

Other:
* Updated ``connection.Connection.post()`` such that if there is a conflict error and a GET does't work on any of the provided aliases, an Exception is raised.
* Updated ``utils.add_alias_prefix()`` to raise an Exception if the lab prefix isn't found.

Page 3 of 5

© 2024 Safety CLI Cybersecurity Inc. All Rights Reserved.