Comments (4)
trvrb
commented on May 28, 2024
Very cool idea. Thoughts on making this "safe" so that unwanted sequences don't end up in the final database...
Could upload to test database rather than vdb. Or better yet, we could think about making a vdb_staging database that would mirror tables within the vdb database and there could be a script to copy vdb_staging into vdb.
from fauna.
trvrb
commented on May 28, 2024
This is a great direction. I'm going to shelve for the moment. Now that the data is basically working, we could start to think about smarter upload scripts. This should integrate well with the overall nextstrain pipeline.
from fauna.
chacalle
commented on May 28, 2024
If the VIPR had an API we could automate the search and download we're doing for ZIKA and other viruses in the future.
from fauna.
trvrb
commented on May 28, 2024
Yes. This would be awesome.
from fauna.
Related Issues (20)
- Suggest using direct clinical sample sequence for MEX_CIENI551 Zika genome
- Annotate titer TSVs with source and passage
- fauna uploads fail in python 3 unicode error HOT 1
- argument parser in upload.py HOT 3
- Migrate to pandas 0.17 HOT 6
- Fauna installation fails for some users who don't run `npm install` inside of `/chateau` HOT 3
- fauna doesn't work with rethinkdb 2.4 HOT 3
- Geographic error? HOT 2
- Switch out `xlrd` HOT 1
- fauna downloads fail with Python 3.10
- PhantomJS not found on PATH - installation via npm install HOT 2
- Set `serum_id` to `lot_number` for CDC titer imports HOT 4
- feat: BV-BRC support HOT 1
- serum_passage_category should be set to "egg" instead of "cell" for CDC human pool data like "L21/22 H3-EGG HUMAN POOL" HOT 7
- Assign correct host to titers from non-ferret hosts (e.g., human and mouse)
- Geolocation assignments fail for duplicate location names HOT 2
- Replace nextstrain remote with aws commands
- Automate backup of Fauna databases to S3 HOT 4
- Support ingest of individual-level human serology data for seasonal flu viruses
- Revisit tdb/upload's `index_fields` HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from fauna.