Skip to content
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

Automate building of all internal databases #1149

Open
dkoslicki opened this issue Dec 7, 2020 · 5 comments
Open

Automate building of all internal databases #1149

dkoslicki opened this issue Dec 7, 2020 · 5 comments
Assignees
@chunyuma @amykglen
Labels
needs discussion

Comments

@dkoslicki
Copy link
Member

Maybe using snakemake, automate the building of all internal databases. Options should include --all, or --<specific database(s)>.
finnagin added a commit that referenced this issue Jan 4, 2021
@finnagin
#1149, added argument to specify config.json field
2a082d5
finnagin added a commit that referenced this issue Jan 4, 2021
@finnagin
#1149, added argument to specify config.json fields for KG1 & KG2
457f380
finnagin added a commit that referenced this issue Jan 4, 2021
@finnagin
#1149, defined pathlist
a9ce1b5
finnagin added a commit that referenced this issue Jan 4, 2021
@finnagin
#1149, added Snakefile
5254643
finnagin added a commit that referenced this issue Jan 4, 2021
@finnagin
#1149, added node_synonymizer rule
e12024c
finnagin added a commit that referenced this issue Jan 4, 2021
@finnagin
#1149, added curie_to_pmids rule
75d5fc1
finnagin added a commit that referenced this issue Jan 4, 2021
@finnagin
#1149, added cohd_database rule
9b96cac
finnagin added a commit that referenced this issue Jan 4, 2021
@finnagin
#1149, added dtd_prob rule
a618144
@finnagin finnagin mentioned this issue Jan 8, 2021
Closed
finnagin added a commit that referenced this issue Jan 12, 2021
@finnagin
#1149
203a1b8
finnagin pushed a commit that referenced this issue Jan 12, 2021
#1149
2c59081
finnagin added a commit that referenced this issue Jan 12, 2021
@finnagin
#1149
c846e49
finnagin added a commit that referenced this issue Jan 12, 2021
@finnagin
#1149, added logs
8291909
finnagin added a commit that referenced this issue Jan 12, 2021
@finnagin
#1149
2e7bfc7
finnagin added a commit that referenced this issue Jan 13, 2021
@finnagin
#1149, fixed pubmed xml path
542fd43
@finnagin
Copy link
Member

TODO: resurrect this issue and make sure the things that were implemented still work. Also to update to refresh databases rather than a fresh build

@dkoslicki
Copy link
Member Author

Still TODO to decrease the amount of manual intervention required to refresh databases. Adding @chunyuma and @amykglen as additional databases have since been created (eg. DTD)

@dkoslicki dkoslicki assigned chunyuma and amykglen and unassigned finnagin Jun 5, 2022
@dkoslicki
Copy link
Member Author

6/22 AHM: as part of KG2/c, all databases are auto-built save for: NGD, COHD, DTD. NGD @amykglen's purview, COHD + DTD @chunyuma's

@saramsey
Copy link
Member

saramsey commented Jun 19, 2024 •
edited
Loading

OK to close, @dkoslicki ?

@dkoslicki
Copy link
Member Author

Hard to say: it would be great to have the build of all databases automated, but that seems like a heavy lift.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@chunyuma chunyuma

@amykglen amykglen

Labels
needs discussion
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
5 participants
@saramsey @dkoslicki @chunyuma @finnagin @amykglen