WormBase / WormBase/ACKnowledge
Where do entities go
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- JavaScript
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Description
Need to discuss what happens with strains, alleles, transgenes - this was from June 2020
Strains, alleles Hinxton outcome
New strains and alleles added by authors via AFP:
Request new names in the name service via automated script
Can be a cronjob disconnected from AFP. The cronjob will take a daily dump from AFP submitted data and will request a WBstrain and WBVariation ID to the name server.
The same script will take anything in the afp_otherstrain and afp_othervariation and add them to the new pap_tables pap_strain and pap_allele once the corresponding WBID is generated
for all the new objects sent by authors
Existing strains recognized by AFP and validated by authors
Need to store paper to strain and paper to allele connections in postgres.
Need to make new pap_strain, pap_allele and pap_transgene tables. They can get dumped with the paper.ace file.
The paper editor needs to be modified to allow edits for strain, allele and transgene lists
Every entity coming via AFP pipeline will have the AFP evidence code
We can use the Person_evidence in the Evidence model
We need to modify the model and add a Text field for Person_Evidence
Update papers.ace dumper to include pap_aftcontributor value as well as Person_evidence ?Person Text (e.g. WBPerson1843 afp) for each entity verified by an author during afp
pap_afpcontributor stores email addresses, but will be updated to now store WBPerson IDs to more easily dump evidence and also not to multiply count WBPersons who may use different email addresses
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by mapping the AFP pipeline, paper editor, entity models, and papers.ace dumper mentioned in the issue. Review how strains, alleles, transgenes, evidence, and contributor data currently move through those areas. Done means the requested tables, author editing, evidence fields, name-service flow, and dump output are specified and implemented together.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- javascript, postgresql
- Domain
- backend, databases
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100