Skip to content

Cloning history updates #492

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Draft
manulera wants to merge 22 commits into
base: master
Choose a base branch
from
Draft

Cloning history updates #492

manulera wants to merge 22 commits into from

Conversation

@manulera
Copy link
Collaborator

@manulera manulera commented Dec 5, 2025

Things to be addressed:

  • What happens with Genbank class and should it handle so many different inputs. What happens if the user provides the start but not the end.

BjornFJohansson and others added 22 commits November 7, 2025 17:21
@BjornFJohansson @manulera
created stubs UploadedFileSource and RepositoryIdSource
5d0cf65
@BjornFJohansson @manulera
next step
4ea5941
@BjornFJohansson @manulera
next step2
27307e3
@BjornFJohansson @manulera
added rudimentary source/history for local files read in reader/parse…
7164964 
…r and sequences downloaded from genbank.
@BjornFJohansson @manulera
fixed fields in model
b6c5fb4
@manulera
enable higher opencloning-linkml versions
1e817b4
@manulera
support and test edge case from #488
5a6c7d3
@manulera
starting to work on better serialization
5028df8
@manulera
simplify serialization to avoid having to use kwargs, instead define …
c22d42d 
…serializer for non-native fields
@manulera
fix tests (happens because TARGET_MODEL was not behaving properly in …
7d89f65 
…SequenceCutSource before)
@manulera
update notebook output
4404482
@manulera
add some repositories
e5d5270
@manulera
add the rest of the models
b47b060
@manulera
add and test oligonucleotide hybridization
242bc4d
@manulera
update to latest model version
2dfd703
@manulera
comment Location out
e95e860
@manulera
fix existing genbank test and adapt to OpenCloning/OpenCloning_LinkML#71
ff396f5
@manulera
update linkml model
d3dd8a9
@manulera
update linkml model and drop repository_name field
edb1521
@manulera
add location serializer to GenomeCoordinatesSource
6a29aa9
@manulera
update opencloning-linkml to released version
a2feb17
@manulera
add utility to get coordinates in the format used for the NCBI API
6f25090
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

No reviews

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

3 participants

@manulera @BjornFJohansson