pombase / pombase-chado-json Goto Github PK
View Code? Open in Web Editor NEWRead a PomBase Chado database and write it as JSON
License: MIT License
Read a PomBase Chado database and write it as JSON
License: MIT License
Dependabot can't resolve your Rust dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
error: failed to parse manifest at `/home/dependabot/dependabot-updater/dependabot_tmp_dir/Cargo.toml`
Caused by:
editions are unstable
Caused by:
feature `edition` is required
this Cargo does not support nightly features, but if you
switch to nightly channel you can add
`cargo-features = ["edition"]` to enable this feature
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
You can mention @dependabot in the comments below to contact the Dependabot team.
Create a table for each top level key in the current JSON file. Create two columns: ID and json_blob. Use compression.
Then change the server code to query SQLite instead of holding everything in memory - big job.
Current top level keys:
Exception, because it is not a map:
In the mini-curation feed on the front page there are publications that are still in progress like:
Instead of failing when a user tries a query.
This also helps a Babraham issue: sometimes the database isn't available the first time a container is started.
Replace the Perl code.
They look like this in the contig files like: /db_xref="SPD:50/50G04"
We should store just the annotation IDs in the terms and genes. There is a lot of duplication in the JSON file especially for term because we including annotation from descendent on term pages.
The same annotation ID appears twice in the annotations array for one of the terms in the SPBC776.02c JSON. This duplicate is discarded by the web code but we should find out what the cause is:
{
"term": "FYPO:0005450",
"is_not": false,
"annotations": [
237667,
237667
],
"summary": [
{
"genotype_uniquenames": [
"dis1-288-unknown-unknown-expression-not_assayed__dis2-11-unknown-unknown-expression-not_assayed__dis2delta__dis3-54-P509L-amino_acid_mutation-expression-not_assayed__ppa1delta__ppe1delta__sds21delta"
]
}
]
},
The gene details need to be added to genes_by_uniquename.
eg. https://www.pombase.org/gene/SPBC725.16 for "binds promoter of cdc22" the identifier in Chado is "SPAC1F7.05-promoter"
Currently if JSON file generation fails we end up with broken web site. We need to monitor the process and only update the site if the load looks good and JSON generation works.
We'll only update the "beta" site from the nightly load.
Dependabot can't resolve your Rust dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
error: failed to parse manifest at `/home/dependabot/dependabot-updater//dependabot_tmp_dir/Cargo.toml`
Caused by:
editions are unstable
Caused by:
feature `edition` is required
this Cargo does not support nightly features, but if you
switch to nightly channel you can add
`cargo-features = ["edition"]` to enable this feature
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
You can mention @dependabot in the comments below to contact the Dependabot team.
We need to write out the files that aren't static so we can update the FTP site each night.
So we can add a message on the allele pages saying that the allele is obsolete / has no annotation.
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.