marius-mather

Synonyms not returned in OLS search API

1

I'm attempting to use Mondo via the OLS API, particularly the search endpoint as I'd like to get good results if users enter synonyms for terms, as well as showing...

Help with configuring ontologies to support synonyms in OLS

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I'm trying to work with a few different ontologies via the OLS search API. For my purposes, if I could search by synonym and get synonyms returned in the search...

As part of developing https://ahida.sydney.edu.au/ and https://omia.org/home/ I've been putting together a [Python client for OLS](https://github.com/ahida-development/ols-py). It's still somewhat early in development, and not all endpoints have been implemented yet,...

polars.lit() not working correctly in polars.fold()? Doesn't expand to the shape of the columns

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### Polars version checks - [X] I have checked that this issue has not already been reported. - [X] I have confirmed this bug exists on the [latest version](https://pypi.org/project/polars/) of...

#### ALL software version info From `hv.show_versions()`: ``` Python : 3.12.2 | packaged by conda-forge | (main, Feb 16 2024, 20:54:21) [Clang 16.0.6 ] Operating system : macOS-14.4.1-arm64-arm-64bit Panel comms...

**Is your feature request related to a problem? Please describe.** As far as I can tell, there is no way to retrieve multiple terms with a single API call, even...

Return annotations in search endpoint via `fieldList`

3

In the OLS3 search API it was possible to request individual annotation fields be included in the results via `fieldList`. You could either include `annotations_trimmed`, or specify an annotation by...

Support transcript identifiers (in parentheses) in variants

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The HGVS nomenclature now recommends including both a sequence and transcript identifier for some variants, with the transcript identifier in parentheses e.g.: https://hgvs-nomenclature.org/stable/recommendations/DNA/substitution/. A similar issue came up previously with...

Link to an external profile when user accounts are managed by a single OIDC provider

3

When user accounts are managed through a single OIDC provider, we want to disable editing of username/email address/password within Galaxy and have them managed at the OIDC provider. This PR...

bug: get_object_identifier returns Enum instance instead of string value for Enum primary keys

1

### Checklist - [x] The bug is reproducible against the latest release or `master`. - [x] There are no similar issues or pull requests to fix it yet. ### Describe...