broadinstitute / gene-hints Goto Github PK
View Code? Open in Web Editor NEWDiscoverability for gene search :dna: :mag:
Home Page: https://broad.io/gene-hints
License: BSD 3-Clause "New" or "Revised" License
Discoverability for gene search :dna: :mag:
Home Page: https://broad.io/gene-hints
License: BSD 3-Clause "New" or "Revised" License
Gene Hints updates popularity data each day via GitHub Actions workflow. The workflow fails like so:
100%|██████████| 180/180 [05:35<00:00, 1.87s/it]
100%|██████████| 180/180 [05:35<00:00, 1.87s/it]/home/runner/work/_temp/3996971a-eb39-4aaf-91b7-d4ed401873fb.sh: line 1: 1619 Killed python gene_hints/gene_hints.py
Output to: ./pubmed_citations/data/tmp/prev_timeframe/2021_01_20.tsv
Error: Process completed with exit code 137.
Another discussion of this error indicates the cause:
Exit code 137 = Out of memory. Therefore I guess your implementation makes the runner (ou docker container) runs out of memory.
Refine the Gene Hints pipeline so GitHub Actions workflows reliably succeed.
Wikipedia page view trends for human genes are updated each day, and written to data/homo-sapiens-wikipedia-trends.tsv
. However, the UI ultimately fetches data/homo-sapiens-gene-details.tsv
, which contains both those trends and PubMed citation count trends.
To get daily updates for data used by the UI, we first need to automate daily updates for PubMed trends.
The code to produce PubMed trends is in /creating_citation_counts_tsv
. Use GitHub Actions to run that code to produce daily updates for PubMed trends data. It might help to create a script that wraps those various shell and Python files, then call the wrapper from GitHub Actions.
The number of page views for a given gene's article on Wikipedia can change due to factors that affect all genes, e.g. weekends.
To normalize for such factors, let's sort genes in https://raw.githubusercontent.com/broadinstitute/gene-hints/main/data/homo-sapiens-gene-details.tsv by view_rank_delta
.
Wikidata — a project related to Wikipedia — has a service that would allow us to get Wikipedia page title given the gene symbol. It uses a powerful but little-known query language called SPARQL. This would allow us to robustly and quickly determine Wikipedia article names from our known gene data, which is important for getting Wikipedia page view trends for those genes.
Tasks:
Like #11, but sort all non-homo-sapiens files by rank_delta
(which we might want to call citation_rank_delta
).
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