Caralyn Reisle

TypeError running cell extraction with downloaded model

6

I am probably doing something incorrect here but I am not sure what. I got everything to run up to and including the combine script, `src/baseline/retriever/combine_retrieval.py`. I then downloaded the...

Show progress of labels without "checked"

1

For users where they are selecting a label it would be nice to show how many examples they have selected a label for as well as those where a label...

Multi-Sentence Classification

2

I am hoping for a clear way to add classification labels for entailment. I'd like to be able to put the claim/hypothesis/sentence1 and evidence/text/sentence2 to display in separate text boxes....

Blank page on clicking "start annotation"

1

How to reproduce the behaviour --------- - Create a new text classification project (single label) using the default admin user (started doccanno via docker as directed in the README). -...

### Describe the bug I am trying to export a realm to a JSON file from the latest jboss/keycloak docker container but I am running into permissions errors. I suspect...

Add an optional compression step (default true) to MAVIS outputs since MAVIS can output a lot of files

Test using pyfaidx instead of Biopython for loading reference FASTA files

4

Loading FASTA files with biopython is quite sloe (~30s). Test whether we can replace the biopython load with using the [pyfaidx](https://pypi.org/project/pyfaidx/) library instead I copied the current function that uses...

Use textwrap.dedent instead of breaking indenting for long strings https://docs.python.org/3/library/textwrap.html#textwrap.dedent

Add out of frame vs in-frame labels for the obvious cases. Leave as not specified for the complex fusions for which this annotation does not necessarily make sense. This should...

Since we are using pytest instead of nose we can use the pytest style bare assert statements instead of self.assertEqual and subclassing unittest